LOCUS       NZ_CP091618             4267 bp    DNA     circular CON 28-JAN-2024
DEFINITION  Salmonella enterica strain 1653 plasmid p1653-3, complete sequence.
ACCESSION   NZ_CP091618
VERSION     NZ_CP091618.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN25270678
            Assembly: GCF_026873365.1
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  JOURNAL   Unpublished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 13:38:11
            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)                     :: 4,773
            CDSs (total)                      :: 4,658
            Genes (coding)                    :: 4,529
            CDSs (with protein)               :: 4,529
            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)              :: 129
            CDSs (without protein)            :: 129
            Pseudo Genes (ambiguous residues) :: 0 of 129
            Pseudo Genes (frameshifted)       :: 48 of 129
            Pseudo Genes (incomplete)         :: 92 of 129
            Pseudo Genes (internal stop)      :: 30 of 129
            Pseudo Genes (multiple problems)  :: 38 of 129
            Pseudo Genes (short protein)      :: 1 of 129
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP091618.1.
            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="1653"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:28901"
                     /plasmid="p1653-3"
                     /geo_loc_name="China: Hangzhou"
                     /collection_date="2021-07"
                     /collected_by="Meina Yue"
     gene            complement(127..276)
                     /locus_tag="L5511_RS23835"
                     /old_locus_tag="L5511_23845"
     CDS             complement(127..276)
                     /locus_tag="L5511_RS23835"
                     /old_locus_tag="L5511_23845"
                     /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            840..971
                     /locus_tag="L5511_RS23900"
     CDS             840..971
                     /locus_tag="L5511_RS23900"
                     /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            complement(1191..2000)
                     /locus_tag="L5511_RS23840"
                     /old_locus_tag="L5511_23850"
     CDS             complement(1191..2000)
                     /locus_tag="L5511_RS23840"
                     /old_locus_tag="L5511_23850"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010222407.1"
                     /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(1993..3243)
                     /locus_tag="L5511_RS23845"
                     /old_locus_tag="L5511_23855"
     CDS             complement(1993..3243)
                     /locus_tag="L5511_RS23845"
                     /old_locus_tag="L5511_23855"
                     /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"
     gene            complement(3655..4023)
                     /locus_tag="L5511_RS23850"
                     /old_locus_tag="L5511_23860"
     CDS             complement(3655..4023)
                     /locus_tag="L5511_RS23850"
                     /old_locus_tag="L5511_23860"
                     /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"
     Typing          complement(270..486)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.781"
                     /coverage="100.0"
                     /evalue="4.32e-80"
     Typing          433..949
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.192"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gggaaaaatg ggatttttcg tttatacgtg taatacgcaa ggtattacag tcaaccgtaa
       61 ttacatgaaa ataaagaaat aagatgtaat accaccgtat tacacatacg ctggccagcg
      121 aaaaagctat aacgcttccc gaccgacagg aggcccggaa tccaccgggg cgtgcaggtt
      181 atcttcagta accttcgcca ttaaatcaaa aaggtcatac tcgccgggaa gctgcgtatc
      241 agcagcatcc cgttgttcat catgttcaga tggcatgggg tgatatccag tagctgagag
      301 gttgttagcg ggtttcgggg cgcagccctg aaccagtcac gtagcgctag cggagtgtat
      361 actggcttag tatgttacgg cgagatggag attcggggaa gtgcttcatg tggcaagggg
      421 gaaaatacgg ctgcggggcg taagtgcaaa atgcaggtaa cgatgaaatg acgcctcctc
      481 gctcactcgg tcgctgcgct cctgccgtga gactgcggcg ggcgttacca gctcacgaag
      541 gacgagataa cgagattgcg ctcaagtcag gaaagtcagg aaaaaggatg cggcgttgcc
      601 gtttttccat aggctccgcc cccctgacaa gcatcacaaa atctgacgct caaatcagtg
      661 gtggcgaaac ccgacaggac tataaagatc ccaggcgttt ccccctggta gctccctcgt
      721 gcgctctcct gttcctgcct ttcggtttac cggtgtcatt ccgctgttat ggccgcgttt
      781 gtctcattcc acgcctgaca ctcagttccg ggtaggcagt tcgctccaag ctggactgta
      841 tgcacgaacc ccccgttcag tccgactgct gcgccttgtc cggtaactat cgtcttgagt
      901 ccaacccgga aagacatgca aaagcgccac tggcagcagc cactggtaat cggattcacg
      961 gagcggagta gagttatcta cagagttctt gaagtggtgg cctgactacg gctacactga
     1021 aaggacagtt ttggtatctg cgctccgtga aagccagtta ccttcggaag aaagagttgg
     1081 tagctctaaa ttccggcaaa cgaaccaccg ttggtagcgg tggttttttt gtttacggct
     1141 taggagatta cggctagaac gaaaggatct caagaagatc ctctcagaaa ttatacagac
     1201 atgcggtagt ttgagatgtc agagctatct aactcttttg ccggaaccag tttgtaatgc
     1261 ctttcctcaa tcaatttcac ttgtccttcg tctatcttta gctcaaacag tgcaatcaaa
     1321 tcgctcgaaa caaactgagc ggaaatagct ctacatctaa catttgggta tttttgttca
     1381 caccacgctg tatcttgcga tgtttgcacc attgatattt gatctgtccc accttttgct
     1441 tgaactggta ttatataatg gcaaccgtat ttatctatac ctacataaag ttcatcgatc
     1501 tctatttgac caattccctt caccgtagtt cttaaatgat tctgtaaaga atatgtggtt
     1561 atacctagaa atatatctat tagccggtta tatctcacct tcgccagcaa tgcctgctcg
     1621 tcgtctaaag aataacctgt aattatctcc ggggtattgt ctggaatttt tattgccacc
     1681 atattaggat ttggcaaaat cctactaata gttactaatc taaatcgata ctttgaccta
     1741 ccagccagct caataatcca ctccttacct tctggctgag tcaacagaat actttctggc
     1801 ataggcgttc taaatctgat tgaatatata acatcaccaa cattagatgg gagttctata
     1861 cctaaatctt ttgcagcact gtttatctct aacctttcaa acaaaacctc taagtcacca
     1921 tcaacatatt tatcgaaaaa tatcttttct accaactgat ggtatctatt tttggacctt
     1981 tcttttttat ccttactcac aaacaacctc cttgttacta ttttttattc tcttagcaat
     2041 tacatttgat gacacaccaa acatagatgc agcatcggac atagaaatag caaccaaact
     2101 ttcatcaccg agtttgattt tcttcgttgg tttttttggc gtaacaccaa gaaccttcat
     2161 aatctgcaag ccaacacttc tagctagcat aggaggaaca ctattaccga cctgtctaaa
     2221 tccatgccac ttagtcacat gaaatctgaa ccaatcagga tatgaatgca gtcttgctgc
     2281 ctctctgacc gtgatgaccc taggatagat cggatgtata ggacgaggag atgtaaaagc
     2341 acctctgtca cttgctgttc ctgcccttaa agtattacat agcccattca tcgagagctt
     2401 tttaaacctg ctgattggtt ctaccgtgtc aggcaaagtt tcaacaaacc gccctctaga
     2461 aatgtcagag tgatctgtca gtaaagaaca cgttaatttg tctttattaa aaatccttgg
     2521 gtagctaaaa tcactaggat cttttcctac gccatgcaaa taggatgagt atagtgattg
     2581 ctcaccaaat ttagcataaa cccaatctct accccatagc tcaggatatt tttccgcatc
     2641 aggaatatcc ccaatagcgt ccccaaccgt tgttctaatg gataatggct cagggtatga
     2701 tggcagagca attcctttcc ttccccccat taagaaaaga cgacggcgat cttgaggaac
     2761 tccataatca gctgcgttta gcactttata atcgcttaca acgtcgtacc cgccatcttt
     2821 aaatgcatcc attatctcta ctaaaaactg cttatgctta ccaaccgtca acccttttac
     2881 attttcaaaa ataaagtatt taggctttag ctcaagaacc agccgtacat agtgatagac
     2941 cagtttgttt ctatcatcat caagcgcgcg ttttcctatt aatgaaaagc cttggcaggg
     3001 agcgcctccg atcactacat caatctcttt ctcaccaata cctgaaactt ccctaacgta
     3061 ttctccggta acatcaacaa cacttctaca tatcgttttg cacataggaa agttatattt
     3121 gtgagcagag caatgtattg gatctatttc aactgatgcc attatatcaa agccagcttg
     3181 ctcgaaaccg agactcagcc cacccgctcc agcaaataaa tcaacagcaa tcggtctagt
     3241 cattctttac acccacgtta tataaaatca acatgatgct atcagaaaaa cgatcgcttt
     3301 accgatcgtt tttctgattt cgattgaaca taacatccct tgcgtgcacc acctgagagg
     3361 ccctcagggc gtttctgacg ggaaaccggc aaaacaggca acaaaccacc cgaaaacccg
     3421 ccagaaacgc gcaggctctg tttttacggc atgcatgagt atgcgcgcaa gtgcatagcg
     3481 cggaaattca cgccattcag ccggggtaag tcctgtttcc ggcgttcttc ccatccgaaa
     3541 acggtgaacg ggcgggaaat ttattgcgtg gccgtgaggc gttggcaaga acatcaggca
     3601 tgaagataag ggggcggatg tacgaacgtt tcacaaaaca atttcgagtg gaaatcagaa
     3661 ccccttcctc ctgccaatgc tatccctcaa tgactcagcc agtctttgag attcatcttc
     3721 cactcttctg aagtcattca cggacagaaa aaaaccattc tctggcgcgc ctgctacaga
     3781 aacagatttt tctgtagcag gcaaagaatc cgctgtagcg agagacgatc catctgtatt
     3841 ttttctcaac ctgtaaagag ccttatcaaa cgcaacctgt gagatcttca gaccgtaacg
     3901 ttcattcagt acagccacaa tttctctcct ggggatgcca tttttcttcc agttttctat
     3961 atcagccagg gaatctctga cagccgcaat cgctgttctt ggaccaaggt taaaattcgc
     4021 catacgccac ccataatgtc ttatcaatgt ctcattttag tccaaaatat cacagaatgt
     4081 cttataattg tcctatcctt gtctttcacg gttcatgtag ccatgaaccg gcaggtatgt
     4141 aacgcttttt tatttcgctc aggcctgcca gatatagatt catgccttaa aagccaagtt
     4201 gctttatccc ttaaatggtc atacaccata cgcaatcgcg atttcatcgc aactgcatga
     4261 atcaaat
//
