LOCUS       NZ_CP091623             4267 bp    DNA     circular CON 28-JAN-2024
DEFINITION  Salmonella enterica strain 1419 plasmid p1419-1, complete sequence.
ACCESSION   NZ_CP091623
VERSION     NZ_CP091623.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN25270676
            Assembly: GCF_026873405.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica
  ORGANISM  Salmonella enterica
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 4267)
  AUTHORS   Ruan,Z.
  TITLE     Genome sequence of Salmonella Goldcoast recovered from children
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4267)
  AUTHORS   Ruan,Z.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-JAN-2022) Department of Clinical laboratory, Sir Run
            Run Shaw Hospital, School of Medicine, Zhejiang University, 3
            Qingchun East Road, Hangzhou, Zhejiang 310016, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x
            Sequencing Technology :: Oxford Nanopore; Illumina NovaSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/28/2024 13:21:11
            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)                     :: 4,464
            CDSs (total)                      :: 4,349
            Genes (coding)                    :: 4,245
            CDSs (with protein)               :: 4,245
            Genes (RNA)                       :: 115
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 104
            CDSs (without protein)            :: 104
            Pseudo Genes (ambiguous residues) :: 0 of 104
            Pseudo Genes (frameshifted)       :: 45 of 104
            Pseudo Genes (incomplete)         :: 72 of 104
            Pseudo Genes (internal stop)      :: 25 of 104
            Pseudo Genes (multiple problems)  :: 35 of 104
            Pseudo Genes (short protein)      :: 1 of 104
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP091623.1.
            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..4267
                     /organism="Salmonella enterica"
                     /mol_type="genomic DNA"
                     /strain="1419"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:28901"
                     /plasmid="p1419-1"
                     /geo_loc_name="China: Hangzhou"
                     /collection_date="2021-02"
                     /collected_by="Meina Yue"
     gene            join(4168..4267,1..710)
                     /locus_tag="L5509_RS22295"
                     /old_locus_tag="L5509_22310"
     CDS             join(4168..4267,1..710)
                     /locus_tag="L5509_RS22295"
                     /old_locus_tag="L5509_22310"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015160340.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_044525163.1"
                     /translation="MSKDKKERSKNRYHQLVEKIFFDKYVDGDLEVLFERLEINSAAKD
                     LGIELPSNVGDVIYSIRFRTPMPESILLTQPEGKEWIIELAGRSKYRFRLVTISRILPN
                     PNMVAIKIPDNTPEIITGYSLDDEQALLAKVRYNRLIDIFLGITTYSLQNHLRTTVKGI
                     GQIEIDELYVGIDKYGCHYIIPVQAKGGTDQISMVQTSQDTAWCEQKYPNVRCRAISAQ
                     FVSSDLIALFELKIDEGQVKLIEERHYKLVPAKELDSSDISNYRMSV"
                     /name="hypothetical protein"
     gene            complement(930..1061)
                     /locus_tag="L5509_RS22355"
     CDS             complement(930..1061)
                     /locus_tag="L5509_RS22355"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /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_072013439.1"
                     /translation="MHEPPVQSDCCALSGNYRLESNPERHAKAPLAAATGNRIHGAE"
                     /name="replication initiation protein"
     gene            1625..1774
                     /locus_tag="L5509_RS22300"
                     /old_locus_tag="L5509_22315"
     CDS             1625..1774
                     /locus_tag="L5509_RS22300"
                     /old_locus_tag="L5509_22315"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_164840373.1"
                     /translation="MPSEHDEQRDAADTQLPGEYDLFDLMAKVTEDNLHAPVDSGPPVG
                     REAL"
                     /name="hypothetical protein"
     gene            2145..2513
                     /locus_tag="L5509_RS22305"
                     /old_locus_tag="L5509_22320"
     CDS             2145..2513
                     /locus_tag="L5509_RS22305"
                     /old_locus_tag="L5509_22320"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880027.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_042114977.1"
                     /translation="MANFNLGPRTAIAAVRDSLADIENWKKNGIPRREIVAVLNERYGL
                     KISQVAFDKALYRLRKNTDGSSLATADSLPATEKSVSVAGAPENGFFLSVNDFRRVEDE
                     SQRLAESLRDSIGRRKGF"
                     /name="hypothetical protein"
     gene            2925..4175
                     /locus_tag="L5509_RS22310"
                     /old_locus_tag="L5509_22325"
     CDS             2925..4175
                     /locus_tag="L5509_RS22310"
                     /old_locus_tag="L5509_22325"
                     /EC_number="2.1.1.37"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015160339.1"
                     /GO_function="GO:0003886 - DNA
                     (cytosine-5-)-methyltransferase activity [Evidence IEA];
                     GO:0008168 - methyltransferase activity [Evidence IEA];
                     GO:1904047 - S-adenosyl-L-methionine binding [Evidence
                     IEA]"
                     /GO_process="GO:0006304 - DNA modification [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA cytosine methyltransferase"
                     /protein_id="WP_130574759.1"
                     /translation="MTRPIAVDLFAGAGGLSLGFEQAGFDIMASVEIDPIHCSAHKYNF
                     PMCKTICRSVVDVTGEYVREVSGIGEKEIDVVIGGAPCQGFSLIGKRALDDDRNKLVYH
                     YVRLVLELKPKYFIFENVKGLTVGKHKQFLVEIMDAFKDGGYDVVSDYKVLNAADYGVP
                     QDRRRLFLMGGRKGIALPSYPEPLSIRTTVGDAIGDIPDAEKYPELWGRDWVYAKFGEQ
                     SLYSSYLHGVGKDPSDFSYPRIFNKDKLTCSLLTDHSDISRGRFVETLPDTVEPISRFK
                     KLSMNGLCNTLRAGTASDRGAFTSPRPIHPIYPRVITVREAARLHSYPDWFRFHVTKWH
                     GFRQVGNSVPPMLARSVGLQIMKVLGVTPKKPTKKIKLGDESLVAISMSDAASMFGVSS
                     NVIAKRIKNSNKEVVCE"
                     /name="DNA cytosine methyltransferase"
     Typing          1416..1632
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.781"
                     /coverage="100.0"
                     /evalue="4.32e-80"
     Typing          complement(953..1433)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.925"
                     /coverage="92.0"
                     /evalue="0.0"
ORIGIN
        1 ttgaaaggtt agagataaac agtgctgcaa aagatttagg tatagaactc ccatctaatg
       61 ttggtgatgt tatatattca atcagattta gaacgcctat gccagaaagt attctgttga
      121 ctcagccaga aggtaaggag tggattattg agctggctgg taggtcaaag tatcgattta
      181 gattagtaac tattagtagg attttgccaa atcctaatat ggtggcaata aaaattccag
      241 acaatacccc ggagataatt acaggttatt ctttagacga cgagcaggca ttgctggcga
      301 aggtgagata taaccggcta atagatatat ttctaggtat aaccacatat tctttacaga
      361 atcatttaag aactacggtg aagggaattg gtcaaataga gatcgatgaa ctttatgtag
      421 gtatagataa atacggttgc cattatataa taccagttca agcaaaaggt gggacagatc
      481 aaatatcaat ggtgcaaaca tcgcaagata cagcgtggtg tgaacaaaaa tacccaaatg
      541 ttagatgtag agctatttcc gctcagtttg tttcgagcga tttgattgca ctgtttgagc
      601 taaagataga cgaaggacaa gtgaaattga ttgaggaaag gcattacaaa ctggttccgg
      661 caaaagagtt agatagctct gacatctcaa actaccgcat gtctgtataa tttctgagag
      721 gatcttcttg agatcctttc gttctagccg taatctccta agccgtaaac aaaaaaacca
      781 ccgctaccaa cggtggttcg tttgccggaa tttagagcta ccaactcttt cttccgaagg
      841 taactggctt tcacggagcg cagataccaa aactgtcctt tcagtgtagc cgtagtcagg
      901 ccaccacttc aagaactctg tagataactc tactccgctc cgtgaatccg attaccagtg
      961 gctgctgcca gtggcgcttt tgcatgtctt tccgggttgg actcaagacg atagttaccg
     1021 gacaaggcgc agcagtcgga ctgaacgggg ggttcgtgca tacagtccag cttggagcga
     1081 actgcctacc cggaactgag tgtcaggcgt ggaatgagac aaacgcggcc ataacagcgg
     1141 aatgacaccg gtaaaccgaa aggcaggaac aggagagcgc acgagggagc taccaggggg
     1201 aaacgcctgg gatctttata gtcctgtcgg gtttcgccac cactgatttg agcgtcagat
     1261 tttgtgatgc ttgtcagggg ggcggagcct atggaaaaac ggcaacgccg catccttttt
     1321 cctgactttc ctgacttgag cgcaatctcg ttatctcgtc cttcgtgagc tggtaacgcc
     1381 cgccgcagtc tcacggcagg agcgcagcga ccgagtgagc gaggaggcgt catttcatcg
     1441 ttacctgcat tttgcactta cgccccgcag ccgtattttc ccccttgcca catgaagcac
     1501 ttccccgaat ctccatctcg ccgtaacata ctaagccagt atacactccg ctagcgctac
     1561 gtgactggtt cagggctgcg ccccgaaacc cgctaacaac ctctcagcta ctggatatca
     1621 ccccatgcca tctgaacatg atgaacaacg ggatgctgct gatacgcagc ttcccggcga
     1681 gtatgacctt tttgatttaa tggcgaaggt tactgaagat aacctgcacg ccccggtgga
     1741 ttccgggcct cctgtcggtc gggaagcgtt atagcttttt cgctggccag cgtatgtgta
     1801 atacggtggt attacatctt atttctttat tttcatgtaa ttacggttga ctgtaatacc
     1861 ttgcgtatta cacgtataaa cgaaaaatcc catttttccc atttgattca tgcagttgcg
     1921 atgaaatcgc gattgcgtat ggtgtatgac catttaaggg ataaagcaac ttggctttta
     1981 aggcatgaat ctatatctgg caggcctgag cgaaataaaa aagcgttaca tacctgccgg
     2041 ttcatggcta catgaaccgt gaaagacaag gataggacaa ttataagaca ttctgtgata
     2101 ttttggacta aaatgagaca ttgataagac attatgggtg gcgtatggcg aattttaacc
     2161 ttggtccaag aacagcgatt gcggctgtca gagattccct ggctgatata gaaaactgga
     2221 agaaaaatgg catccccagg agagaaattg tggctgtact gaatgaacgt tacggtctga
     2281 agatctcaca ggttgcgttt gataaggctc tttacaggtt gagaaaaaat acagatggat
     2341 cgtctctcgc tacagcggat tctttgcctg ctacagaaaa atctgtttct gtagcaggcg
     2401 cgccagagaa tggttttttt ctgtccgtga atgacttcag aagagtggaa gatgaatctc
     2461 aaagactggc tgagtcattg agggatagca ttggcaggag gaaggggttc tgatttccac
     2521 tcgaaattgt tttgtgaaac gttcgtacat ccgccccctt atcttcatgc ctgatgttct
     2581 tgccaacgcc tcacggccac gcaataaatt tcccgcccgt tcaccgtttt cggatgggaa
     2641 gaacgccgga aacaggactt accccggctg aatggcgtga atttccgcgc tatgcacttg
     2701 cgcgcatact catgcatgcc gtaaaaacag agcctgcgcg tttctggcgg gttttcgggt
     2761 ggtttgttgc ctgttttgcc ggtttcccgt cagaaacgcc ctgagggcct ctcaggtggt
     2821 gcacgcaagg gatgttatgt tcaatcgaaa tcagaaaaac gatcggtaaa gcgatcgttt
     2881 ttctgatagc atcatgttga ttttatataa cgtgggtgta aagaatgact agaccgattg
     2941 ctgttgattt atttgctgga gcgggtgggc tgagtctcgg tttcgagcaa gctggctttg
     3001 atataatggc atcagttgaa atagatccaa tacattgctc tgctcacaaa tataactttc
     3061 ctatgtgcaa aacgatatgt agaagtgttg ttgatgttac cggagaatac gttagggaag
     3121 tttcaggtat tggtgagaaa gagattgatg tagtgatcgg aggcgctccc tgccaaggct
     3181 tttcattaat aggaaaacgc gcgcttgatg atgatagaaa caaactggtc tatcactatg
     3241 tacggctggt tcttgagcta aagcctaaat actttatttt tgaaaatgta aaagggttga
     3301 cggttggtaa gcataagcag tttttagtag agataatgga tgcatttaaa gatggcgggt
     3361 acgacgttgt aagcgattat aaagtgctaa acgcagctga ttatggagtt cctcaagatc
     3421 gccgtcgtct tttcttaatg gggggaagga aaggaattgc tctgccatca taccctgagc
     3481 cattatccat tagaacaacg gttggggacg ctattgggga tattcctgat gcggaaaaat
     3541 atcctgagct atggggtaga gattgggttt atgctaaatt tggtgagcaa tcactatact
     3601 catcctattt gcatggcgta ggaaaagatc ctagtgattt tagctaccca aggattttta
     3661 ataaagacaa attaacgtgt tctttactga cagatcactc tgacatttct agagggcggt
     3721 ttgttgaaac tttgcctgac acggtagaac caatcagcag gtttaaaaag ctctcgatga
     3781 atgggctatg taatacttta agggcaggaa cagcaagtga cagaggtgct tttacatctc
     3841 ctcgtcctat acatccgatc tatcctaggg tcatcacggt cagagaggca gcaagactgc
     3901 attcatatcc tgattggttc agatttcatg tgactaagtg gcatggattt agacaggtcg
     3961 gtaatagtgt tcctcctatg ctagctagaa gtgttggctt gcagattatg aaggttcttg
     4021 gtgttacgcc aaaaaaacca acgaagaaaa tcaaactcgg tgatgaaagt ttggttgcta
     4081 tttctatgtc cgatgctgca tctatgtttg gtgtgtcatc aaatgtaatt gctaagagaa
     4141 taaaaaatag taacaaggag gttgtttgtg agtaaggata aaaaagaaag gtccaaaaat
     4201 agataccatc agttggtaga aaagatattt ttcgataaat atgttgatgg tgacttagag
     4261 gttttgt
//
