LOCUS       NZ_CP038598             4448 bp    DNA     circular CON 05-JUN-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Hadar strain 12-2388
            plasmid p12-2388.3, complete sequence.
ACCESSION   NZ_CP038598
VERSION     NZ_CP038598.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN06030204
            Assembly: GCF_004768645.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Hadar
  ORGANISM  Salmonella enterica subsp. enterica serovar Hadar
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 4448)
  AUTHORS   Robertson,J., Lin,J., Wren-Hedegus,A., Arya,G., Carrillo,C. and
            Nash,J.H.E.
  TITLE     Development of a multi-locus typing scheme for an Enterobacteriaceae
            linear plasmid that mediates inter-species transfer of flagella
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4448)
  AUTHORS   Robertson,J., Lin,J., Wren-Hedegus,A., Arya,G., Carrillo,C. and
            Nash,J.H.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-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. 4.5
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 60.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_004768645.1-RS_2024_06_05
            Annotation Date                   :: 06/05/2024 01:02:17
            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)                     :: 4,555
            CDSs (total)                      :: 4,433
            Genes (coding)                    :: 4,299
            CDSs (with protein)               :: 4,299
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 16
            Pseudo Genes (total)              :: 134
            CDSs (without protein)            :: 134
            Pseudo Genes (ambiguous residues) :: 0 of 134
            Pseudo Genes (frameshifted)       :: 70 of 134
            Pseudo Genes (incomplete)         :: 82 of 134
            Pseudo Genes (internal stop)      :: 25 of 134
            Pseudo Genes (multiple problems)  :: 40 of 134
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP038598.1.
            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..4448
                     /organism="Salmonella enterica subsp. enterica serovar
                     Hadar"
                     /mol_type="genomic DNA"
                     /strain="12-2388"
                     /serovar="Hadar"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:149385"
                     /plasmid="p12-2388.3"
                     /geo_loc_name="Canada"
                     /collected_by="NML"
     gene            join(4136..4448,1..11)
                     /locus_tag="CVJ63_RS23115"
                     /old_locus_tag="CVJ63_23115"
     CDS             join(4136..4448,1..11)
                     /locus_tag="CVJ63_RS23115"
                     /old_locus_tag="CVJ63_23115"
                     /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_170949721.1"
                     /translation="MLTMWVTEDEHRRLLERCDGRQLAAWMRQTCLDEKPARTGKLPSI
                     SPALLRQLAGMGNNLNQIARRVNAGGGTGHDRVQIVAALMAIDAGLEQLRHAVLEKGTD
                     DDH"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            220..>654
                     /locus_tag="CVJ63_RS23675"
                     /pseudo=""
     CDS             220..>654
                     /locus_tag="CVJ63_RS23675"
                     /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            689..1180
                     /locus_tag="CVJ63_RS23310"
     CDS             689..1180
                     /locus_tag="CVJ63_RS23310"
                     /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_063844470.1"
                     /translation="MSSLLTLAKDLEQKSKAQQQSTGEMLKAAFSEHEQSVRAELSASA
                     RRISDAISAHEQSMSEAMEKNRRSVLLTAGRAWLTILMVSALLIATSGSILWWQGQQIT
                     DNYTHLRQQEDTLAKMTARTWGVRYQESSDGRRFLILPPGMQAEAIPYDGTTWIRLKQE
                     "
                     /name="MbeB family mobilization protein"
     gene            1187..1402
                     /locus_tag="CVJ63_RS23315"
     CDS             1187..1402
                     /locus_tag="CVJ63_RS23315"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137422.1"
                     /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_044704874.1"
                     /translation="MTELEKQLLTALEQLHQDYSQRLDEWESAFAEWQKMSGLMQRENA
                     VLNERVSDLSTQVLSLSEQLRRLSGN"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2094..2321)
                     /locus_tag="CVJ63_RS23125"
                     /old_locus_tag="CVJ63_23125"
     CDS             complement(2094..2321)
                     /locus_tag="CVJ63_RS23125"
                     /old_locus_tag="CVJ63_23125"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010615788.1"
                     /GO_component="GO:0005886 - plasma membrane [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="YgdI/YgdR family lipoprotein"
                     /protein_id="WP_000719360.1"
                     /translation="MKKIFVSVFAAAVALSALTGCTRTSYAIHTNDGRTIVSDGKPTES
                     DSGLLGYKDANGVKQQINKADVKEVSEIPH"
                     /name="YgdI/YgdR family lipoprotein"
     gene            complement(2343..2576)
                     /locus_tag="CVJ63_RS23130"
                     /old_locus_tag="CVJ63_23130"
     CDS             complement(2343..2576)
                     /locus_tag="CVJ63_RS23130"
                     /old_locus_tag="CVJ63_23130"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008461706.1"
                     /GO_component="GO:0005886 - plasma membrane [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="YgdI/YgdR family lipoprotein"
                     /protein_id="WP_044704865.1"
                     /translation="MNKKTLLAAMMVALVTFAAAGCSSNQEIKTTDGRTIVTDGKPKVD
                     SDTGLVSYKDAHTGRTEQINRDKITNMSELDN"
                     /name="YgdI/YgdR family lipoprotein"
     gene            2736..3104
                     /locus_tag="CVJ63_RS23135"
                     /old_locus_tag="CVJ63_23135"
     CDS             2736..3104
                     /locus_tag="CVJ63_RS23135"
                     /old_locus_tag="CVJ63_23135"
                     /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_044704866.1"
                     /translation="MALLISLVVVAGLYYQFWYKPHRAPILRIWGIAPDGQEFRLLLTE
                     HGEKEAVLLFGKKSFVAVPDTQNLYGGCYYLYLEDAHKNELLIELNESDLYPGGAIELQ
                     HNGGRKIHCEILKVRWSR"
                     /name="hypothetical protein"
     gene            complement(3341..3499)
                     /locus_tag="CVJ63_RS23825"
                     /old_locus_tag="CVJ63_23140"
     CDS             complement(3341..3499)
                     /locus_tag="CVJ63_RS23825"
                     /old_locus_tag="CVJ63_23140"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032670878.1"
                     /translation="MHEPPVQSDCCALSGNYRLESNPERHEKSLLAAAISNWRYTRDKL
                     RGLEVWA"
                     /name="hypothetical protein"
     Typing          3952..4030
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.75"
                     /coverage="100.0"
                     /evalue="2.7400000000000003e-32"
     Typing          complement(3388..3876)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.345"
                     /coverage="94.0"
                     /evalue="1.69e-147"
     Typing          2..1494
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="90.8"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          4137..4447
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.308"
                     /coverage="97.0"
                     /evalue="3.78e-59"
ORIGIN
        1 atgatcatta aatttcatcc gcgcggtcgc ggcggtggcg ccgggccggt ggactatttg
       61 ctgggtaaag accggcagcg tgaaggcgcc accgtcctgc agggcaagcc ggaagaagtc
      121 cgggagctga ttgatgtgtc gccttacgtg aagaaataca cctccggcgt actgtcgttt
      181 gcggaggcag atctgcctcc cggccagcgg gaaaaactga tggccagctt cgagcgtgtt
      241 ctgatgcccg gcctcgataa agatcagtac agcattctgt gggtggagca cgcggacaag
      301 gggcgtctgg agctgaactt tctgatcccc aataccgagc tgctgaccgg caggcggctc
      361 cagccgtact acgaccgcgc cgaccggccg cgcatcgatg cctggcagac ggtggtcaac
      421 ggccggctgg ggctgcacga cccgaacgcg ccggaaaacc ggcgggcgct ggtcacgccg
      481 tccgcgctgc cggaagcgaa gcaggaagct gcccaggcga ttacgcgcgg cctgcttgcc
      541 cttgcctcat ccggggagct gaaaacccgt caggacgtca ctgaggcgct ggaaagcgca
      601 ggttttgagg tggtgcgcag cacgaaaagc agcatcagca ttgccgaccc ggacgggggg
      661 cgaaacatcc gactgaaggg agccatctat gagcagtctt ttaacgctgg cgaaggactt
      721 ggagcagaaa tcgaaagcgc agcagcagag taccggcgag atgctgaaag ccgcattcag
      781 cgagcacgag cagtctgtca gagcggaact gagcgcaagc gcgaggagaa tcagcgacgc
      841 catcagcgcc cacgaacaga gtatgagcga ggcgatggag aaaaaccggc ggagcgtgct
      901 gctgacagcc gggagggcat ggctcaccat cctgatggtg tcagcgctgc tgatcgccac
      961 gagcgggagc attctgtggt ggcaggggca gcagataacc gacaattaca cacatcttcg
     1021 tcagcaggaa gataccctgg cgaaaatgac tgcccggacg tggggagtgc gctatcagga
     1081 gagcagcgac ggccggaggt tccttatcct gccgccgggg atgcaagccg aagccatccc
     1141 ctacgacggg acgacctgga tccgcctgaa acaggagtag cggaaaatga cagagctgga
     1201 aaagcagttg ctgaccgcat tagagcagct acatcaggac tactcgcaaa ggctggacga
     1261 atgggagagc gccttcgcgg aatggcagaa gatgtctggg cttatgcaac gggagaacgc
     1321 ggtgctgaac gagcgcgtgt cggacttgag cacgcaggtg ctgagtttaa gcgagcagct
     1381 gcgccgcttg tccgggaact gaatgccacc gagttccggc agggggagaa tgagtatcag
     1441 aaaacactgg agctggagcg ccagccgcag aaaacctaca aaggaccgac gctgggctga
     1501 cggatgccgg cccgtgataa accccaagaa gaagggctgc gaaattcccc gctaaatacg
     1561 tcgtgatgca aagatcacgg cctataccag ggggaattat gaaactgctt aatgttattg
     1621 aagctgtact taactgcctg catctggcgg cagaactgtg ggagtggctg gaaaagcatt
     1681 tgccggtttt cggggccttc acgctgtttt tgggctgaat cctgccgtca ttcacctggc
     1741 tgcatggcta tgcagtcggg taaaaattat ctcccggctt aacggaggat gtagcgttgc
     1801 ttaagccggg ttttcgggtg ccaggtgccg tctgcgccgt cagtgccgat ccggcggtgc
     1861 agacaacgga tgttatggta aaagcatgat gcctggcggg tacggaaaaa ttgtggcgac
     1921 cgagcctgca gacgcaaaaa tccggcccat acttattcgt ctccttcatc aggaatgcag
     1981 tactatccag ccactgcagg tatttggccc ccagcggggg ctttttttgc ctgttgttgg
     2041 ggcagataaa gaaaagggcc gcattagcgg cccttttcgg agagagcgat gcctcaatgc
     2101 ggaatttcag agacttcttt aacgtcggct ttattgatct gctgtttgac accatttgcg
     2161 tctttatagc ccagcaggcc tgagtctgat tctgtaggct tgccgtcgct gacaattgta
     2221 cgcccgtcgt tggtgtggat ggcatagctt gtgcgcgtgc agccggttag ggctgaaagc
     2281 gcaactgccg ctgcgaacac tgaaacaaaa atctttttca aagccagctc cttttatccg
     2341 tatcagttgt ctagttcact catgttggta attttgtcac ggttgatctg ttcggttcgg
     2401 cctgtatggg catctttgta ggatactaac cccgtatcac tgtcaacttt gggtttgccg
     2461 tctgtaacga tagtgcgacc atctgtggtt tttatttctt ggtttgaaga acatccagca
     2521 gcggcaaagg tcaccaacgc gaccatcatg gccgccaaca gcgttttttt attcataata
     2581 ggttccctgc ttaaaggtaa agtggatatg gtcactaacc atctaagtat aggtcgtttt
     2641 ttcatgcgaa aagaggattg aaggtgggca tcatgcccag cagtaaaaat gaatgaaaaa
     2701 cgattttgga atgttgcttg tttttgagga ttgaaatggc cttattaatt tcactggttg
     2761 tagtggcagg tctttactat caattttggt ataagccaca tagagcgccg atcttgcgta
     2821 tatgggggat cgcgcctgat ggacaagaat ttcgattatt gctaacagag catggagaaa
     2881 aagaggctgt tttactgttc ggaaagaaat cttttgttgc cgtgccagat acgcagaacc
     2941 tttatggtgg gtgttattac ctttatttag aggatgctca caagaacgag cttttaattg
     3001 agttaaacga aagtgattta taccccggtg gcgcaataga acttcaacac aacggcggtc
     3061 ggaagattca ttgcgagata ctaaaagtaa ggtggagtcg ttaactcaag taatgtttcc
     3121 taagtatgtt gataggcaaa catagtggta gttagtctct ctgagtaaat gatcttcttg
     3181 tgatcctgtc gttacagtcg taatctcttg ctctgaaaac gaaaaaacca cctggggagg
     3241 tggtttgatc gaaggttaag tcagttgggg aactgcttaa ccaggtaact gggtatacga
     3301 gaccgcagaa accaaaaatg ttctttcagt gtagcctctc tcaggcccat acttcaagac
     3361 ctcttaattt gtctctcgta tacctccagt tactaatggc tgctgccagt agcgattttt
     3421 cgtgtctttc cgggttggac tcaagacgat agttaccgga taaggcgcag cagtcggact
     3481 gaacgggggg ttcgtgcata cagtcaatcc tggagcgaac tgccttcgcg gaactgagtg
     3541 tcaggcgtgg aatgagaaac cgcggccata acagcggaat gacaccggta aaccgaaagg
     3601 caggaatgcg ggggagcacg agggagccat cagggggaaa cgcctggtat ctttaagccg
     3661 catcgggttt cgccaccact gatttgagcg tcagattctg tgatgcttgt caggggggcg
     3721 gagcctatgg aaaaccggca gcgccgcatc cttttttccc ctcctgcatt cacgtatttc
     3781 ccccccacgt ctttatccgt gagtccgtac cgctcgccgc agccgaacga ccgagcgtag
     3841 cgagtcagtg agcgaggaag cggaatatcc accgggacag gcatcagccc cttacgcacc
     3901 tgagcctcat ctcacagttt ttatgactga ctatttcatc ccgattcccg tcgtgccacc
     3961 atagtaagcc agtatacact ccgctagcgc tacgtgactg gttcagggct gcgccccgaa
     4021 acccgccaaa agcctgacgc gcctgcggct tgtccaaccc cgcgccgacc gggaaaggct
     4081 ttcccgcccg tcccggcgtt atcaggagac cggtttgtca gagaaacgga acaagatgct
     4141 caccatgtgg gtgacggagg acgagcaccg gcggctgctc gaacgctgtg acggcaggca
     4201 gctggcggcg tggatgcggc agacctgtct tgatgaaaag cctgcgcgta ccggaaagct
     4261 accctcgatc tcgccggcgc tgctgcgcca gcttgccggc atgggcaaca acctgaacca
     4321 gatagcccgc cgcgttaacg ccggcggcgg taccggccat gacagggtgc agattgtggc
     4381 ggcgctgatg gcaatcgatg ccggccttga gcagctgcgg cacgccgttc ttgagaaagg
     4441 aacggacg
//
