LOCUS       NZ_CP064913             4700 bp    DNA     circular CON 03-SEP-2023
DEFINITION  Salmonella enterica subsp. enterica strain C18 plasmid pC18-4k,
            complete sequence.
ACCESSION   NZ_CP064913
VERSION     NZ_CP064913.1
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 4700)
  AUTHORS   Huang,T.-W.
  TITLE     Whole-genome sequencing of ceftriaxone-resistant Salmonella enterica
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4700)
  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
            CP064913.1.
            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..4700
                     /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="pC18-4k"
                     /geo_loc_name="Taiwan"
                     /collection_date="1999-11"
     gene            join(4604..4700,1..218)
                     /locus_tag="IYN89_RS23985"
                     /old_locus_tag="IYN89_23800"
     CDS             join(4604..4700,1..218)
                     /locus_tag="IYN89_RS23985"
                     /old_locus_tag="IYN89_23800"
                     /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_308416251.1"
                     /translation="MPPNCVSSMSGRWSTRKRWSWSDHSGSERITARRCDNRIKRGFRR
                     VSALKAGAIHPAAWLCSPGKFTGRKRDGLPGALLRVLPGRHPIRAEPAWSGAGKRCYGK
                     "
                     /name="hypothetical protein"
     gene            492..761
                     /locus_tag="IYN89_RS23990"
                     /old_locus_tag="IYN89_23805"
     CDS             492..761
                     /locus_tag="IYN89_RS23990"
                     /old_locus_tag="IYN89_23805"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_019080654.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_024143071.1"
                     /translation="MNQTMSQKLARDSLGNAQTFEGGVYVTKNGVAELFIQTAAERDAE
                     VREMREERNINALFKLATLAKKEITEGKGMTPEEVLGRLRAARK"
                     /name="hypothetical protein"
     gene            776..1114
                     /locus_tag="IYN89_RS23995"
                     /old_locus_tag="IYN89_23810"
     CDS             776..1114
                     /locus_tag="IYN89_RS23995"
                     /old_locus_tag="IYN89_23810"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012822260.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_040117006.1"
                     /translation="MSQQYTVSIAPMAYQCLADIESYKSGYIGSLKAGDLVDNLLQESV
                     ACIIQDPERYHYNFHLQDRGMLLRERLDVESEYRVLYDFDGTNIEILLFVSMKQDFEKQ
                     LYRYNLLN"
                     /name="hypothetical protein"
     gene            complement(1215..1802)
                     /locus_tag="IYN89_RS24000"
                     /old_locus_tag="IYN89_23815"
     CDS             complement(1215..1802)
                     /locus_tag="IYN89_RS24000"
                     /old_locus_tag="IYN89_23815"
                     /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_020833680.1"
                     /translation="MIRKIFFASAIVIAISGCTAMDKLAGMGVVSQQTSTFDNSTVIEV
                     SPNSLYDPNSTWGTQLQLGAIWSSAYPEEVGLILSYNSNVSSGNAAYLGLTGIDINIDG
                     KISSYKAQQQTNLSSSAYNSVSKTIYTSSKNTVVIPYKLLESMVSAKNCRIRIHTSQGN
                     QDIDFSAQSIPGGKATAIVSIKEFMVKVESFK"
                     /name="hypothetical protein"
     gene            2883..3206
                     /locus_tag="IYN89_RS24005"
                     /old_locus_tag="IYN89_23820"
     CDS             2883..3206
                     /locus_tag="IYN89_RS24005"
                     /old_locus_tag="IYN89_23820"
                     /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_306726704.1"
                     /translation="MLTLWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGTGHDRVQVVAALMAIDAGLERLRHAVLEKGAE
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3415..>3849
                     /locus_tag="IYN89_RS24010"
                     /pseudo=""
     CDS             3415..>3849
                     /locus_tag="IYN89_RS24010"
                     /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            3884..4381
                     /locus_tag="IYN89_RS24015"
                     /old_locus_tag="IYN89_23830"
     CDS             3884..4381
                     /locus_tag="IYN89_RS24015"
                     /old_locus_tag="IYN89_23830"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001086853.1"
                     /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_308416250.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQTTGEMLKAAFSEHEKSVRAELNESE
                     KRISAAILDHDRKLSSAMSQRTKGMVRMVSQTWLTIVLVSALLIASSAGILWWQGQQML
                     DNYTSIREQKDALEKLNARTWGVRYQEDNQGRFLVLPEGVKADTNWTFDNGRKNGIRLV
                     QE"
                     /name="MbeB family mobilization protein"
     gene            4388..4603
                     /locus_tag="IYN89_RS24020"
                     /old_locus_tag="IYN89_23835"
     CDS             4388..4603
                     /locus_tag="IYN89_RS24020"
                     /old_locus_tag="IYN89_23835"
                     /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_063617430.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLSNG"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          2596..2774
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.803"
                     /coverage="83.0"
                     /evalue="1.5900000000000002e-64"
     Typing          complement(2135..2613)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.918"
                     /coverage="92.0"
                     /evalue="4.5400000000000006e-173"
     Typing          3197..4698
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="90.818"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gtcgctgtga taaccggata aaacggggct ttcggcgggt ttctgcgctg aaagccggag
       61 ccattcaccc ggctgcatgg ctatgcagtc cggggaaatt taccggacgc aaacgggacg
      121 gtttaccggg tgctttgctg cgggttttac ccggcaggca ccctatccgc gccgaacctg
      181 cctggagcgg tgcgggcaag agatgttatg gtaaatgatt ctgaattaaa ctaattttcc
      241 cttctttcac ctttctgtgt aaaaatatgt actcaattta tacaccaact gataaactct
      301 attcaaagca cggacactgg ccaccatgtg ccatagcgag aatttgtact ggcctaataa
      361 atcaacactg aaacctgaaa cctgaaacct gaaacctgaa acctgaaacc tgaaaccgga
      421 aactatgacc cttgaatcgt gcagcgccgt tctcgccgga agcgccccta tatgatgaga
      481 aaaaaatgcc tatgaaccag accatgtccc agaaactcgc aagagacagt ctcggaaatg
      541 cacaaacctt tgaaggaggt gtttacgtca ctaaaaacgg agtagctgag ttattcatcc
      601 aaaccgcagc agaacgtgat gctgaagttc gtgagatgag agaagaacgc aatatcaacg
      661 ccctttttaa gctggcaacg ttggctaaaa aggaaatcac agaaggcaaa ggcatgaccc
      721 cagaagaggt cttagggagg ttgcgtgccg ctagaaaata acagagaggt gtttagtgtc
      781 ccagcaatac acggtttcaa tcgcgccgat ggcatatcaa tgtttagctg atatcgagtc
      841 ttacaagagt ggatacattg ggtcactcaa ggccggtgat ctggttgata acttacttca
      901 ggaatcagtt gcctgcatta tccaagaccc tgaacgttat cactacaatt tccacttaca
      961 ggatcgaggt atgcttttac gtgagcggct cgatgttgag agtgaataca gggtgcttta
     1021 cgattttgac ggaacgaaca tcgaaatact gttgtttgtg agcatgaagc aggattttga
     1081 aaagcagctg tatcgctata atttgctgaa ttaacactaa acacccggca tcgtcgggtt
     1141 ttttcgtgca gacaaaaatt tccacctatg cctattaaca ctaagttagt agatataggt
     1201 gggcttacgt gtccttattt aaaactttcg actttgacca tgaactcttt aatggaaacg
     1261 atcgctgtcg ctttacctcc agggatgctt tgcgccgaga agtcgatgtc ttgatttcct
     1321 tggcttgtgt gtatgcgaat gcggcagttt ttagctgata ccatgctctc cagcaattta
     1381 taggggataa caacagtgtt cttgctagag gtatagatcg ttttagatac ggagttatat
     1441 gcgctgctgc ttagattagt ttgctgctgt gctttatagc tggatatttt gccatcaata
     1501 tttatatcaa tccccgtcaa acctaagtat gcggcatttc cgctagatac attcgagttg
     1561 taggaaagaa ttagcccaac ctcttctgga taggcactag accatatcgc gcccaactga
     1621 agttgtgttc cccaagtgct gttaggatcg tatagcgaat ttggagatac ctctataacg
     1681 gtcgagttat caaaggttga tgtttgctga gaaacaacac ccattcctgc caatttatcc
     1741 attgctgtac agccagagat ggctattacg attgcagaag caaaaaaaat ctttcttatc
     1801 atttttttga cctttttggt ttgtttgcca gagagtgaaa tagcatttta tttctgaaac
     1861 tatcttgaag gcttatagct gttttaaaca gtgttttgaa cacagagttg aaggatcttc
     1921 ttgagatcct cgggtgggag tcgtaatctc ttgacccaga aacgaaaaaa ccacctgggg
     1981 aggtggtttt tcgatggttc agtaagttgg ggaacttctg aaccgtggta acagggtgta
     2041 caagaccgct gccaccaaat tcgtccttcc agtttagccg tagttgggct gatacttcaa
     2101 gaactctgcg ttagtaatct cttgtacatc ctcttaccaa tggctgctgc cagtggcgat
     2161 aagtcgtgtc tttccgggtt ggactcaaga tgatagttac cggataaggc gcagcggtcg
     2221 gactgaacgg ggggttcgtg catacagtcc agcttggagc gaactgccta cccggaactg
     2281 agtgtcaggc gtggaatgag aaaccgcggc cataacagcg gaatgacacc ggtaaaccga
     2341 aaggcaggaa caggagagcg catgagggag ctaccagggg gaaacgcctg ggatctttat
     2401 agtcctgtcg ggtttcgccg ccactgattt gagcgtcaga tttcgtgatg cttgtcaggg
     2461 gggcggagcc tatggaaaaa cggcatcgcc gcatcctttt cctgtcttct ccaatttgag
     2521 tgcgacctgc ttatcccgtc atctgcgagc cggtaacgcc cgccgcagtc tcacggcagg
     2581 agcgcagcga ccgagtgagc gaggaggcgt catttcatct tcactggcat gtcgcactga
     2641 cgccccgcag ctgcatttcc tcccatcaca tgaagcactt tcataaatta ccactccgcc
     2701 gtaacatatt tagccagtat acactccgct agcgctacgt gactggttca gggctgcgcc
     2761 ccgaaacccg ctaaaagcca ctgacgcgcc tgcggcttgt ccaaccccgc gccgaccggg
     2821 aaaggatttc ccgtccgtcc cggggttgtc aggaggcctg attgtcagag aaacgcacca
     2881 aaatgctcac cctgtgggtg acggaagacg agcaccggcg actgctggag cgctgcgacg
     2941 gcaaacagct tgcagcgtgg atgcgccaga catgcctgga cgagaagccc gctcgcgccg
     3001 gcaaacttcc gtcaatctcg ccggcgctgc ttcgtcagct cgccggcatg ggaaacaacc
     3061 tcaaccagat tgcccggcag gttaacgccg gtggcggtac cgggcacgac cgtgtgcagg
     3121 ttgtcgccgc gctaatggcc atcgatgccg gactcgaacg gctgcggcac gccgtgctgg
     3181 aaaagggggc agaggatgat cgttaaattc catcccagag ggcgcggcgg tggcgccggt
     3241 ccggtggatt acctgctggg gaaagaccgg cagcgtgacg gcgccagcgt tctgcagggt
     3301 aagccggagg aagtccggga gcttattgac gcctcgccct acgccaaaaa gtacacatcc
     3361 ggggtgctgt cgtttgcgga acaggactta ccgcccgggc agcgcgaaaa gctgatggcg
     3421 agctttgagc gtgttctgat gcccggactc gataaggacc agtacagcgt gctgtgggtt
     3481 gagcaccagg acaaagggcg actggagctg aacttcctga tcccgaacac ggagctgctg
     3541 accggcagac gtctccagcc gtattacgac cgcgccgacc gtccgcgcat tgatgcctgg
     3601 cagaccatag tgaacggcag gctggggctg cacgacccga acgcgccgga aaaccggcgg
     3661 gcgctggtca cgccttccgc gctgccggaa gcgaagcagg aggtcgccca ggcgattacg
     3721 cgcggcctgc ttgcccttgc ctcatccggg gagctgaaaa cccgtcagga cgtcactgag
     3781 gcgctggaaa gcgcaggttt cgaggtggtg cgcaccacga aaagcagcat cagcattgcc
     3841 gacccggatg gggggcgaaa catccgactc aagggagcca tctatgaaca gtcttttaac
     3901 gctggcgaag gacttagagc agaaatcgaa agcgcagcag cagactaccg gcgagatgct
     3961 gaaagccgca ttcagcgagc acgagaagtc tgtcagagcg gaactgaacg aaagcgagaa
     4021 gagaatcagc gccgccatcc tcgaccacga caggaagctg tcctcagcca tgagccagcg
     4081 cacgaaaggc atggtgcgta tggtcagcca gacgtggctg accatcgtcc tggtctccgc
     4141 gctgctgata gcctcgagcg cgggcattct gtggtggcag gggcagcaga tgctcgacaa
     4201 ttacacgagc atccgggagc agaaggacgc gctggagaag ctgaacgccc ggacgtgggg
     4261 cgtgaggtac caggaagaca accaggggcg ctttctggtg ctgccggaag gcgtgaaagc
     4321 ggacacgaac tggacgttcg acaacggcag gaagaacggc atcagactgg tgcaggagta
     4381 gagcagcatg acggagctgg aaaaacagtt gctgagcgca ttagagcagc tacagcagga
     4441 ctactcgaaa aggctggacg agtgggagaa cgccttcgcg gaatggcgga cgatgtctgg
     4501 tcttatgcaa cgggagaacg cggcgctgag cgagcgcgtc acgggcttga gcaggcaggt
     4561 gcagagtttg agcgagcagc tgcgccggtt gtcgaacggc tgaatgccgc cgaactgcgt
     4621 cagcagcatg agcgggcgct ggagcaccag aaagcgctgg agctggagcg atcacagcgg
     4681 cagcgaacgt ataacggccc
//
