LOCUS       NZ_CP060848             4267 bp    DNA     circular CON 24-MAY-2024
DEFINITION  Salmonella enterica strain 733 plasmid p733-3, complete sequence.
ACCESSION   NZ_CP060848
VERSION     NZ_CP060848.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15941598
            Assembly: GCF_022559425.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica
  ORGANISM  Salmonella enterica
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 4267)
  AUTHORS   Yue,M. and Ruan,Z.
  TITLE     Whole genome sequencing of Salmonella enterica serotype Goldcoast
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4267)
  AUTHORS   Yue,M. and Ruan,Z.
  TITLE     Direct Submission
  JOURNAL   Submitted (30-AUG-2020) 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
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022559425.1-RS_2024_05_24
            Annotation Date                   :: 05/24/2024 04:18:53
            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)                     :: 4,763
            CDSs (total)                      :: 4,649
            Genes (coding)                    :: 4,523
            CDSs (with protein)               :: 4,523
            Genes (RNA)                       :: 114
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 83
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 126
            CDSs (without protein)            :: 126
            Pseudo Genes (ambiguous residues) :: 0 of 126
            Pseudo Genes (frameshifted)       :: 47 of 126
            Pseudo Genes (incomplete)         :: 91 of 126
            Pseudo Genes (internal stop)      :: 29 of 126
            Pseudo Genes (multiple problems)  :: 37 of 126
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP060848.1.
            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="733"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:28901"
                     /plasmid="p733-3"
                     /geo_loc_name="China: Hangzhou"
                     /collection_date="2019-08"
                     /collected_by="Meina Yue"
     gene            529..678
                     /locus_tag="IAR32_RS23800"
                     /old_locus_tag="IAR32_23620"
     CDS             529..678
                     /locus_tag="IAR32_RS23800"
                     /old_locus_tag="IAR32_23620"
                     /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            1049..1417
                     /locus_tag="IAR32_RS23805"
                     /old_locus_tag="IAR32_23625"
     CDS             1049..1417
                     /locus_tag="IAR32_RS23805"
                     /old_locus_tag="IAR32_23625"
                     /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            1829..3079
                     /locus_tag="IAR32_RS23810"
                     /old_locus_tag="IAR32_23630"
     CDS             1829..3079
                     /locus_tag="IAR32_RS23810"
                     /old_locus_tag="IAR32_23630"
                     /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            3072..3881
                     /locus_tag="IAR32_RS23815"
                     /old_locus_tag="IAR32_23635"
     CDS             3072..3881
                     /locus_tag="IAR32_RS23815"
                     /old_locus_tag="IAR32_23635"
                     /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(4101..4232)
                     /locus_tag="IAR32_RS23890"
     CDS             complement(4101..4232)
                     /locus_tag="IAR32_RS23890"
                     /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"
     Typing          320..536
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.781"
                     /coverage="100.0"
                     /evalue="4.32e-80"
     Typing          complement(2..337)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.349"
                     /coverage="92.0"
                     /evalue="1.0599999999999999e-114"
     Typing          complement(3893..4267)
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="83.204"
                     /coverage="99.0"
                     /evalue="4.03e-89"
ORIGIN
        1 tgagtgtcag gcgtggaatg agacaaacgc ggccataaca gcggaatgac accggtaaac
       61 cgaaaggcag gaacaggaga gcgcacgagg gagctaccag ggggaaacgc ctgggatctt
      121 tatagtcctg tcgggtttcg ccaccactga tttgagcgtc agattttgtg atgcttgtca
      181 ggggggcgga gcctatggaa aaacggcaac gccgcatcct ttttcctgac tttcctgact
      241 tgagcgcaat ctcgttatct cgtccttcgt gagctggtaa cgcccgccgc agtctcacgg
      301 caggagcgca gcgaccgagt gagcgaggag gcgtcatttc atcgttacct gcattttgca
      361 cttacgcccc gcagccgtat tttccccctt gccacatgaa gcacttcccc gaatctccat
      421 ctcgccgtaa catactaagc cagtatacac tccgctagcg ctacgtgact ggttcagggc
      481 tgcgccccga aacccgctaa caacctctca gctactggat atcaccccat gccatctgaa
      541 catgatgaac aacgggatgc tgctgatacg cagcttcccg gcgagtatga cctttttgat
      601 ttaatggcga aggttactga agataacctg cacgccccgg tggattccgg gcctcctgtc
      661 ggtcgggaag cgttatagct ttttcgctgg ccagcgtatg tgtaatacgg tggtattaca
      721 tcttatttct ttattttcat gtaattacgg ttgactgtaa taccttgcgt attacacgta
      781 taaacgaaaa atcccatttt tcccatttga ttcatgcagt tgcgatgaaa tcgcgattgc
      841 gtatggtgta tgaccattta agggataaag caacttggct tttaaggcat gaatctatat
      901 ctggcaggcc tgagcgaaat aaaaaagcgt tacatacctg ccggttcatg gctacatgaa
      961 ccgtgaaaga caaggatagg acaattataa gacattctgt gatattttgg actaaaatga
     1021 gacattgata agacattatg ggtggcgtat ggcgaatttt aaccttggtc caagaacagc
     1081 gattgcggct gtcagagatt ccctggctga tatagaaaac tggaagaaaa atggcatccc
     1141 caggagagaa attgtggctg tactgaatga acgttacggt ctgaagatct cacaggttgc
     1201 gtttgataag gctctttaca ggttgagaaa aaatacagat ggatcgtctc tcgctacagc
     1261 ggattctttg cctgctacag aaaaatctgt ttctgtagca ggcgcgccag agaatggttt
     1321 ttttctgtcc gtgaatgact tcagaagagt ggaagatgaa tctcaaagac tggctgagtc
     1381 attgagggat agcattggca ggaggaaggg gttctgattt ccactcgaaa ttgttttgtg
     1441 aaacgttcgt acatccgccc ccttatcttc atgcctgatg ttcttgccaa cgcctcacgg
     1501 ccacgcaata aatttcccgc ccgttcaccg ttttcggatg ggaagaacgc cggaaacagg
     1561 acttaccccg gctgaatggc gtgaatttcc gcgctatgca cttgcgcgca tactcatgca
     1621 tgccgtaaaa acagagcctg cgcgtttctg gcgggttttc gggtggtttg ttgcctgttt
     1681 tgccggtttc ccgtcagaaa cgccctgagg gcctctcagg tggtgcacgc aagggatgtt
     1741 atgttcaatc gaaatcagaa aaacgatcgg taaagcgatc gtttttctga tagcatcatg
     1801 ttgattttat ataacgtggg tgtaaagaat gactagaccg attgctgttg atttatttgc
     1861 tggagcgggt gggctgagtc tcggtttcga gcaagctggc tttgatataa tggcatcagt
     1921 tgaaatagat ccaatacatt gctctgctca caaatataac tttcctatgt gcaaaacgat
     1981 atgtagaagt gttgttgatg ttaccggaga atacgttagg gaagtttcag gtattggtga
     2041 gaaagagatt gatgtagtga tcggaggcgc tccctgccaa ggcttttcat taataggaaa
     2101 acgcgcgctt gatgatgata gaaacaaact ggtctatcac tatgtacggc tggttcttga
     2161 gctaaagcct aaatacttta tttttgaaaa tgtaaaaggg ttgacggttg gtaagcataa
     2221 gcagttttta gtagagataa tggatgcatt taaagatggc gggtacgacg ttgtaagcga
     2281 ttataaagtg ctaaacgcag ctgattatgg agttcctcaa gatcgccgtc gtcttttctt
     2341 aatgggggga aggaaaggaa ttgctctgcc atcataccct gagccattat ccattagaac
     2401 aacggttggg gacgctattg gggatattcc tgatgcggaa aaatatcctg agctatgggg
     2461 tagagattgg gtttatgcta aatttggtga gcaatcacta tactcatcct atttgcatgg
     2521 cgtaggaaaa gatcctagtg attttagcta cccaaggatt tttaataaag acaaattaac
     2581 gtgttcttta ctgacagatc actctgacat ttctagaggg cggtttgttg aaactttgcc
     2641 tgacacggta gaaccaatca gcaggtttaa aaagctctcg atgaatgggc tatgtaatac
     2701 tttaagggca ggaacagcaa gtgacagagg tgcttttaca tctcctcgtc ctatacatcc
     2761 gatctatcct agggtcatca cggtcagaga ggcagcaaga ctgcattcat atcctgattg
     2821 gttcagattt catgtgacta agtggcatgg atttagacag gtcggtaata gtgttcctcc
     2881 tatgctagct agaagtgttg gcttgcagat tatgaaggtt cttggtgtta cgccaaaaaa
     2941 accaacgaag aaaatcaaac tcggtgatga aagtttggtt gctatttcta tgtccgatgc
     3001 tgcatctatg tttggtgtgt catcaaatgt aattgctaag agaataaaaa atagtaacaa
     3061 ggaggttgtt tgtgagtaag gataaaaaag aaaggtccaa aaatagatac catcagttgg
     3121 tagaaaagat atttttcgat aaatatgttg atggtgactt agaggttttg tttgaaaggt
     3181 tagagataaa cagtgctgca aaagatttag gtatagaact cccatctaat gttggtgatg
     3241 ttatatattc aatcagattt agaacgccta tgccagaaag tattctgttg actcagccag
     3301 aaggtaagga gtggattatt gagctggctg gtaggtcaaa gtatcgattt agattagtaa
     3361 ctattagtag gattttgcca aatcctaata tggtggcaat aaaaattcca gacaataccc
     3421 cggagataat tacaggttat tctttagacg acgagcaggc attgctggcg aaggtgagat
     3481 ataaccggct aatagatata tttctaggta taaccacata ttctttacag aatcatttaa
     3541 gaactacggt gaagggaatt ggtcaaatag agatcgatga actttatgta ggtatagata
     3601 aatacggttg ccattatata ataccagttc aagcaaaagg tgggacagat caaatatcaa
     3661 tggtgcaaac atcgcaagat acagcgtggt gtgaacaaaa atacccaaat gttagatgta
     3721 gagctatttc cgctcagttt gtttcgagcg atttgattgc actgtttgag ctaaagatag
     3781 acgaaggaca agtgaaattg attgaggaaa ggcattacaa actggttccg gcaaaagagt
     3841 tagatagctc tgacatctca aactaccgca tgtctgtata atttctgaga ggatcttctt
     3901 gagatccttt cgttctagcc gtaatctcct aagccgtaaa caaaaaaacc accgctacca
     3961 acggtggttc gtttgccgga atttagagct accaactctt tcttccgaag gtaactggct
     4021 ttcacggagc gcagatacca aaactgtcct ttcagtgtag ccgtagtcag gccaccactt
     4081 caagaactct gtagataact ctactccgct ccgtgaatcc gattaccagt ggctgctgcc
     4141 agtggcgctt ttgcatgtct ttccgggttg gactcaagac gatagttacc ggacaaggcg
     4201 cagcagtcgg actgaacggg gggttcgtgc atacagtcca gcttggagcg aactgcctac
     4261 ccggaac
//
