LOCUS       NZ_CP064912             5234 bp    DNA     circular CON 03-SEP-2023
DEFINITION  Salmonella enterica subsp. enterica strain C18 plasmid pC18-5k,
            complete sequence.
ACCESSION   NZ_CP064912
VERSION     NZ_CP064912.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16789119
            Assembly: GCF_031035935.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica
  ORGANISM  Salmonella enterica subsp. enterica
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 5234)
  AUTHORS   Huang,T.-W.
  TITLE     Whole-genome sequencing of ceftriaxone-resistant Salmonella enterica
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5234)
  AUTHORS   Huang,T.-W.
  TITLE     Direct Submission
  JOURNAL   Submitted (13-NOV-2020) Department of Microbiology and Immunology,
            School of Medicine, College of Medicine, Taipei Medical University,
            No. 250, Wuxin Street, Taipei 11031, Taiwan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2019
            Assembly Method                   :: Unicycer v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 150.0x
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/01/2023 16:27:14
            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)                     :: 4,809
            CDSs (total)                      :: 4,689
            Genes (coding)                    :: 4,533
            CDSs (with protein)               :: 4,533
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 156
            CDSs (without protein)            :: 156
            Pseudo Genes (ambiguous residues) :: 0 of 156
            Pseudo Genes (frameshifted)       :: 70 of 156
            Pseudo Genes (incomplete)         :: 103 of 156
            Pseudo Genes (internal stop)      :: 25 of 156
            Pseudo Genes (multiple problems)  :: 40 of 156
            Pseudo Genes (short protein)      :: 1 of 156
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP064912.1.
            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..5234
                     /organism="Salmonella enterica subsp. enterica"
                     /mol_type="genomic DNA"
                     /strain="C18"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:59201"
                     /plasmid="pC18-5k"
                     /geo_loc_name="Taiwan"
                     /collection_date="1999-11"
     gene            join(5097..5234,1..147)
                     /gene="nadS"
                     /locus_tag="IYN89_RS23940"
                     /old_locus_tag="IYN89_23755"
     CDS             join(5097..5234,1..147)
                     /gene="nadS"
                     /locus_tag="IYN89_RS23940"
                     /old_locus_tag="IYN89_23755"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000007431.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NadS family protein"
                     /protein_id="WP_001697687.1"
                     /translation="MSFFDELKASLEEAVEIKNGVREPARVTRYELADVKAIRAQLNVS
                     QSEMAKVLGTSLDTIKSWETGRRNPTGLAAKVLATIQANPKFFQELAAH"
                     /name="nadS"
     gene            341..1246
                     /locus_tag="IYN89_RS23945"
                     /old_locus_tag="IYN89_23760"
     CDS             341..1246
                     /locus_tag="IYN89_RS23945"
                     /old_locus_tag="IYN89_23760"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_019725130.1"
                     /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_085281041.1"
                     /translation="MHNAALELFNDRLPHKPYFSDDLHFGVRIAGKERAILAKYIQFNQ
                     PHAMFWLGFDVDRAGAAIDWSDRNAPAPTLTITNPENGHAHLLYALKTSIRTAPDGKMK
                     PLCYAAAVENALRKKLEADTGYSGLICKNPNHGHWKVAVWQPELYTLDWLADFLDLNAA
                     NEKEIVADYGLGRNCTLFDKTRKWAYRAIRQGWPEYEQWLQACYERASAYNLQFAVPLD
                     ENEVSGIAKSIAKWTSSKFSEESFSDFVKKTHTKKIQSKRGVLSGKSRRIGSLEDTRPW
                     DDLGISRRKYFYMKKNGEGK"
                     /name="replication initiation protein"
     gene            1243..2115
                     /locus_tag="IYN89_RS23950"
                     /old_locus_tag="IYN89_23765"
     CDS             1243..2115
                     /locus_tag="IYN89_RS23950"
                     /old_locus_tag="IYN89_23765"
                     /inference="COORDINATES: protein motif:HMM:NF033610.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF4231 domain-containing protein"
                     /protein_id="WP_088402844.1"
                     /translation="MKYPSLYDVTNKRSASYQKRYFFFLRLEYCILILNAVNAFLTYEK
                     KHIVALVLFSMLMLMMVLKIKKTSEQEWYKYRAITESIKTVSWKFSMRAEPFNDEDEVK
                     NINSLSEYLEDIVGGSEFISKTIDPKSVDESTVTDEMKGLRTLSFEKRRDFYVDGRIND
                     QRDWYVSKAQANKDAGKKWNICMFVIYVLAFLCSLYNAYYSVPGSIIPISILTTIASSL
                     VGWIQVKRYSELSASYILTAHEIGVIKEQASYVSSESDFSSFIRDAETAFSREHTQWIA
                     RRVANRKPK"
                     /name="DUF4231 domain-containing protein"
     gene            complement(2133..2537)
                     /locus_tag="IYN89_RS23955"
                     /old_locus_tag="IYN89_23770"
     CDS             complement(2133..2537)
                     /locus_tag="IYN89_RS23955"
                     /old_locus_tag="IYN89_23770"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_019821692.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="TIR domain-containing protein"
                     /protein_id="WP_085281039.1"
                     /translation="MAREHKVFISHAWAHHDELESLRRLIDARPYFNAEYSEVSRNEPI
                     NSTNAPYIKSVLKRKILDSNILIGLAGIYASHSSWMEWELDTALANGIPVIGVVPRGAQ
                     RISTMVSTRAVEVVRWNTESIIAAIRLHAR"
                     /name="TIR domain-containing protein"
     gene            2824..3150
                     /locus_tag="IYN89_RS23960"
                     /old_locus_tag="IYN89_23775"
     CDS             2824..3150
                     /locus_tag="IYN89_RS23960"
                     /old_locus_tag="IYN89_23775"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006674374.1"
                     /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_000415578.1"
                     /translation="MEKRTKEIKIRLTETEHQRLLDRCDRTHLAEWLRQLGLGEHTSRK
                     RRVPDVAPELLRQVSGIGNNLNQIARRLNQTDSLTPSERASLLVVLTSLDRQLGDLLEQ
                     NRDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3359..>3781
                     /locus_tag="IYN89_RS23965"
                     /pseudo=""
     CDS             3359..>3781
                     /locus_tag="IYN89_RS23965"
                     /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            3828..4313
                     /locus_tag="IYN89_RS23970"
                     /old_locus_tag="IYN89_23785"
     CDS             3828..4313
                     /locus_tag="IYN89_RS23970"
                     /old_locus_tag="IYN89_23785"
                     /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_108490868.1"
                     /translation="MSEILNLAKGFEEKSKQQAQDTELSVKREFARLETSISAELQSSS
                     QSISNAIREQNGRLTGMIRTSVSAAMAWIFLCFALLIGILGGIIWFQGTIITSRLSEMD
                     SYSQQLESLKAKSGAGVTIYSDDKNRNTYLVVLPKQAHGVETYTSTTDNTVVKYTAK"
                     /name="MbeB family mobilization protein"
     gene            4383..4607
                     /locus_tag="IYN89_RS23975"
                     /old_locus_tag="IYN89_23790"
     CDS             4383..4607
                     /locus_tag="IYN89_RS23975"
                     /old_locus_tag="IYN89_23790"
                     /inference="COORDINATES: protein motif:HMM:NF016769.3"
                     /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_223363283.1"
                     /translation="MEKQLLSALESLQTSYEQQQQAWQDSYSSLQHMFETTSQALTHSD
                     RVCQHLSSQVESLRAQVESLSRNVSRLMR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            4763..5095
                     /locus_tag="IYN89_RS23980"
                     /old_locus_tag="IYN89_23795"
     CDS             4763..5095
                     /locus_tag="IYN89_RS23980"
                     /old_locus_tag="IYN89_23795"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015873600.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_085281492.1"
                     /translation="MSHAIEFIETPMFTRQIKQIATDEELRELQKTLIESPDKGDLIQK
                     TGGLRKVRMATGNQGKSGSARVIYFLATTEVIYLVMAYPKSTKDSLTDAEKAALKMLTQ
                     QLKDEV"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     Typing          3141..4699
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.678"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 agtgagatgg cgaaagtgct gggaaccagt ctcgacacca tcaagagctg ggaaaccgga
       61 cgccgtaacc cgactggact ggcggcgaag gtgctggcaa ccatccaggc gaatccaaaa
      121 ttcttccagg agctggcggc gcactaagcc gttgtgacag aaggattcga caggcgaggc
      181 cgctcacgtg taatttaacg gcaacagaaa aaacaaagcc ccggaaatca tgagctatct
      241 tggcggatga gcatgactac cagggccagg tacgaaacct tgaaaggata ttagcacatg
      301 aaccgtgcca gacaacagcc cgccataagc gcagggcaca ttgcataacg ccgcactcga
      361 actttttaac gaccgcttac cgcacaagcc gtacttttcg gacgatctgc actttggtgt
      421 acgcattgcc ggtaaggaac gcgccattct ggcgaaatac attcagttca atcagcctca
      481 cgctatgttc tggctgggat tcgacgtcga tcgcgccggt gccgccatcg actggagtga
      541 ccgcaacgcg cccgcgccca cgctgaccat cactaaccct gaaaatggac acgcgcacct
      601 gctttatgcg ctgaaaacct cgatacgtac cgcgccggac ggaaaaatga agccgctgtg
      661 ctacgccgcc gccgtggaga acgcgctacg taaaaaatta gaggctgaca cggggtattc
      721 gggactaatc tgcaaaaatc cgaaccacgg ccactggaaa gttgccgtat ggcagccgga
      781 actctacacg ctggactggt tggctgattt tcttgatttg aacgccgcga acgagaaaga
      841 aatcgttgcc gactacggat taggccgtaa ctgcacccta ttcgataaaa cccgtaagtg
      901 ggcctatcgc gctatccgtc agggctggcc tgagtatgag cagtggctgc aagcctgcta
      961 cgaacgcgcc agcgcctata atctgcaatt cgcagtaccg ctggatgaaa atgaggttag
     1021 tggaatagct aaaagtattg ctaagtggac ttcatcaaaa tttagtgagg aatcattcag
     1081 cgattttgtt aaaaagacac atacaaaaaa aattcaatca aagagaggtg ttttatcagg
     1141 aaaatcaaga cgaataggta gtctagagga tactcgtccg tgggatgatt tgggcataag
     1201 tagaaggaag tatttttata tgaaaaagaa tggtgaagga aaatgaaata cccaagtctt
     1261 tatgatgtaa caaataaaag atctgcttca tatcagaaaa ggtatttctt ctttttaagg
     1321 cttgaatatt gcattttgat acttaatgcg gtcaatgctt tcttaactta tgaaaaaaaa
     1381 cacatagtcg cattagtact gttctccatg cttatgttaa tgatggtttt aaaaattaaa
     1441 aaaacatcag aacaagagtg gtacaaatac agggcgatta ctgaatcgat aaaaactgtc
     1501 tcatggaagt tttccatgag agctgaacca tttaatgatg aagatgaggt taaaaatata
     1561 aactcattat cagagtatct ggaggatatt gttggtggta gtgagttcat atctaaaact
     1621 attgatccta agtcagtgga tgaaagcacg gtgactgatg agatgaaagg gcttcgaacc
     1681 ctatcatttg aaaagcgcag agacttttat gtagatggaa ggattaatga tcaaagagat
     1741 tggtatgtaa gtaaggctca agcaaacaaa gatgcaggga aaaaatggaa catttgtatg
     1801 ttcgttatct atgtattagc gttcttatgt tcactttata atgcatatta ttcagttcca
     1861 ggtagcataa ttccaataag cattttgaca acaatagcat cgtcattagt aggttggatt
     1921 caagttaaaa ggtatagcga actgtccgct tcgtatattc ttaccgcgca tgaaataggg
     1981 gtaataaaag aacaggcgtc atatgtttca agtgagagtg atttctcctc atttattaga
     2041 gatgcggaaa ctgcattttc gagagagcat acccaatgga ttgctagacg agtagccaac
     2101 agaaaaccga agtaaggggc accgcccctt ttttatcgcg catgaaggcg gattgcagca
     2161 ataatacttt cagtgttcca tctaacaact tctactgctc ttgttgaaac catggtagat
     2221 atccgctgcg cacctcttgg aacaacacct ataacaggta ttccgttagc tagcgcagta
     2281 tctaactccc actccatcca actactatga gatgcataga tgcctgctaa accaatcaag
     2341 atattagaat ctagtatctt tcttttgaga acggatttta tgtacggtgc gttggttgaa
     2401 tttattggtt cattcctgct gacttcggaa tactcagcat taaagtaggg tctagcgtca
     2461 atcaatcttc ttaatgattc cagttcatcg tgatgcgccc atgcatgact aataaaaacc
     2521 ttatgttctc ttgccactga ttgctccttt tactcaatcc cctatgaacg cgcattatac
     2581 ctctgcgccg atccgttttg cactcgaacc tatatcagat aacagcctct cttagagggg
     2641 ccgttttttt tgcagccagc acagaatctg ccatacttca ccttacttta agccagtaca
     2701 cacagcgtcc cctctaacga ggtgccaccg tgactggttc agggggctcg ccgccccccg
     2761 aaacccctgg catccactgc gaaaaattct cacagtggtg cgaatttttt ctcagcggag
     2821 cctatggaaa agcgaacaaa agagatcaaa atccggctca ccgaaactga gcatcagcga
     2881 ctgcttgatc gctgtgaccg gactcatctt gcagagtggc tgcgtcagct tggtctggga
     2941 gaacacacct cacgcaagcg ccgtgtgcct gatgtggctc ccgaacttct gcgacaggtc
     3001 agcgggattg gtaacaacct gaaccagatc gcccgtcgcc tgaaccagac tgattccctg
     3061 acgccttctg aacgtgcctc gctgctcgtc gtactgacca gccttgaccg tcagcttggc
     3121 gacctgctgg agcagaaccg tgatcgttaa aattcactca cggggtgcgg gttcgggcag
     3181 tgggcccgtg gattacctgc tgggtaaaga ccggcagcgc gaacaggccc gcgtactgcg
     3241 cggcaaccct gaacatgtgc gcgagctaat cgacggctgc gactttgccc gcgcctacac
     3301 atctggcgtg ctgtcatttc aggaacctga cattgcagac gcggagaaat cgcgcctgat
     3361 ggacgaatgg gagcacacgc tgctgaccgg cctcgattgt gaccagtacg cctgtctgtg
     3421 ggtagagcat cgcgacaagg gacggcttga gctgaatttt gtcatcccga acatcgaatt
     3481 gcagagcggc aaacgcctgc aaccctactt tgaccgcgct gaccgccccc gtgtcaacgc
     3541 ctggcagacc ctgaccaacg accggctggg gctgcgcgac ccgaacgatc cgacttaccg
     3601 ccgcccgctg acgcaggcca gcgatcttcc ccgcgacaaa cagcaggcgg cagagaaaat
     3661 taccgccggc ctgatgaacc tgatgcagca gggcatgatc cgcagccggc aggacgtggt
     3721 gacgcagctg gaaagctacg gcctgaccgt ggcacgggaa acgaaaagca gcatcagcat
     3781 tgccgatccg gacggcggcc gaaatatccg gctgaaagga atgatatatg agcgagattt
     3841 taaatttggc gaagggcttc gaggagaaat cgaagcagca ggcgcaggat accgagctga
     3901 gcgtgaagcg cgagttcgcg aggctggaga cgtctatcag cgcggaactg caatcaagct
     3961 cgcagagcat cagcaacgct atccgcgagc agaacggcag gctgacgggc atgatcagaa
     4021 cctccgtctc agcggcgatg gcgtggatat tcctctgctt tgccctgctg atcggtatcc
     4081 tgggcgggat aatctggttt cagggcacga tcatcacctc gcgcctgagc gagatggaca
     4141 gctacagcca acagctggag agcctgaaag cgaaaagcgg cgcgggcgtg acgatttaca
     4201 gcgacgacaa gaaccggaac acttacctgg tggtgctgcc gaagcaggcg cacggcgtgg
     4261 aaacctacac atcgacgacc gacaacaccg tggtgaaata cacggcgaaa taaccccgtc
     4321 agaacgccct gaatcgcgac tgagcggttt taagaccgag gatgagcaaa accatgaccg
     4381 agatggaaaa acagcttctg agcgccttag aaagcttaca gacaagttac gagcaacagc
     4441 agcaggcgtg gcaggacagc tacagcagct tgcagcacat gttcgagact acctcacagg
     4501 cgctgacgca cagcgacagg gtgtgtcagc acttgagcag tcaggtagag agcttgcgcg
     4561 cgcaggtcga gagcttgagc aggaacgtca gccgcttgat gcgctgattg cacagcatga
     4621 ccgcgcccgt gaggagaagc tgcgcgagca gcagccggag ccgcagaaaa aaccgacccg
     4681 ctactatggc ccctcgatgt gatcgctttt ccgaattcag attttagtgt actatgtacg
     4741 ccattaaaaa caggagacag ccgtgagtca tgcgattgag tttatcgaga ccccgatgtt
     4801 tacccgtcag ataaaacaga tcgccacgga tgaagagctc agggagctgc aaaagacgct
     4861 gattgagtcg ccggacaaag gcgatctcat ccagaaaacc ggcgggctgc gaaaagtcag
     4921 aatggcgacg ggaaaccagg gaaaaagcgg cagtgcaagg gtgatttact ttctggccac
     4981 caccgaggtg atttatctgg tgatggccta cccgaaaagc accaaagaca gcctgacgga
     5041 cgcggagaaa gccgcgctga agatgctgac ccaacaactg aaagacgagg tgtgacatga
     5101 gtttttttga cgagctgaaa gcatcgctgg aagaagccgt tgaaatcaaa aacggcgtca
     5161 gagagcctgc ccgcgtcacc cgttacgagc tggcagacgt gaaggccatc agggcacagc
     5221 tgaacgtttc acag
//
