LOCUS       NZ_CP060839             4267 bp    DNA     circular CON 24-MAY-2024
DEFINITION  Salmonella enterica strain 852 plasmid p852-3, complete sequence.
ACCESSION   NZ_CP060839
VERSION     NZ_CP060839.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15941601
            Assembly: GCF_022559365.1
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  JOURNAL   Unpublished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_022559365.1-RS_2024_05_24
            Annotation Date                   :: 05/24/2024 04:14:53
            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)                     :: 4,778
            CDSs (total)                      :: 4,662
            Genes (coding)                    :: 4,546
            CDSs (with protein)               :: 4,546
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 116
            CDSs (without protein)            :: 116
            Pseudo Genes (ambiguous residues) :: 0 of 116
            Pseudo Genes (frameshifted)       :: 47 of 116
            Pseudo Genes (incomplete)         :: 80 of 116
            Pseudo Genes (internal stop)      :: 25 of 116
            Pseudo Genes (multiple problems)  :: 32 of 116
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP060839.1.
            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="852"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:28901"
                     /plasmid="p852-3"
                     /geo_loc_name="China: Hangzhou"
                     /collection_date="2019-12"
                     /collected_by="Meina Yue"
     gene            join(4038..4267,1..580)
                     /locus_tag="IAR35_RS23870"
                     /old_locus_tag="IAR35_23720"
     CDS             join(4038..4267,1..580)
                     /locus_tag="IAR35_RS23870"
                     /old_locus_tag="IAR35_23720"
                     /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(800..931)
                     /locus_tag="IAR35_RS23960"
     CDS             complement(800..931)
                     /locus_tag="IAR35_RS23960"
                     /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            1495..1644
                     /locus_tag="IAR35_RS23875"
                     /old_locus_tag="IAR35_23725"
     CDS             1495..1644
                     /locus_tag="IAR35_RS23875"
                     /old_locus_tag="IAR35_23725"
                     /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            2015..2383
                     /locus_tag="IAR35_RS23880"
                     /old_locus_tag="IAR35_23730"
     CDS             2015..2383
                     /locus_tag="IAR35_RS23880"
                     /old_locus_tag="IAR35_23730"
                     /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            2795..4045
                     /locus_tag="IAR35_RS23885"
                     /old_locus_tag="IAR35_23735"
     CDS             2795..4045
                     /locus_tag="IAR35_RS23885"
                     /old_locus_tag="IAR35_23735"
                     /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          1286..1502
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.781"
                     /coverage="100.0"
                     /evalue="4.32e-80"
     Typing          complement(823..1303)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.925"
                     /coverage="92.0"
                     /evalue="0.0"
ORIGIN
        1 aggtaaggag tggattattg agctggctgg taggtcaaag tatcgattta gattagtaac
       61 tattagtagg attttgccaa atcctaatat ggtggcaata aaaattccag acaatacccc
      121 ggagataatt acaggttatt ctttagacga cgagcaggca ttgctggcga aggtgagata
      181 taaccggcta atagatatat ttctaggtat aaccacatat tctttacaga atcatttaag
      241 aactacggtg aagggaattg gtcaaataga gatcgatgaa ctttatgtag gtatagataa
      301 atacggttgc cattatataa taccagttca agcaaaaggt gggacagatc aaatatcaat
      361 ggtgcaaaca tcgcaagata cagcgtggtg tgaacaaaaa tacccaaatg ttagatgtag
      421 agctatttcc gctcagtttg tttcgagcga tttgattgca ctgtttgagc taaagataga
      481 cgaaggacaa gtgaaattga ttgaggaaag gcattacaaa ctggttccgg caaaagagtt
      541 agatagctct gacatctcaa actaccgcat gtctgtataa tttctgagag gatcttcttg
      601 agatcctttc gttctagccg taatctccta agccgtaaac aaaaaaacca ccgctaccaa
      661 cggtggttcg tttgccggaa tttagagcta ccaactcttt cttccgaagg taactggctt
      721 tcacggagcg cagataccaa aactgtcctt tcagtgtagc cgtagtcagg ccaccacttc
      781 aagaactctg tagataactc tactccgctc cgtgaatccg attaccagtg gctgctgcca
      841 gtggcgcttt tgcatgtctt tccgggttgg actcaagacg atagttaccg gacaaggcgc
      901 agcagtcgga ctgaacgggg ggttcgtgca tacagtccag cttggagcga actgcctacc
      961 cggaactgag tgtcaggcgt ggaatgagac aaacgcggcc ataacagcgg aatgacaccg
     1021 gtaaaccgaa aggcaggaac aggagagcgc acgagggagc taccaggggg aaacgcctgg
     1081 gatctttata gtcctgtcgg gtttcgccac cactgatttg agcgtcagat tttgtgatgc
     1141 ttgtcagggg ggcggagcct atggaaaaac ggcaacgccg catccttttt cctgactttc
     1201 ctgacttgag cgcaatctcg ttatctcgtc cttcgtgagc tggtaacgcc cgccgcagtc
     1261 tcacggcagg agcgcagcga ccgagtgagc gaggaggcgt catttcatcg ttacctgcat
     1321 tttgcactta cgccccgcag ccgtattttc ccccttgcca catgaagcac ttccccgaat
     1381 ctccatctcg ccgtaacata ctaagccagt atacactccg ctagcgctac gtgactggtt
     1441 cagggctgcg ccccgaaacc cgctaacaac ctctcagcta ctggatatca ccccatgcca
     1501 tctgaacatg atgaacaacg ggatgctgct gatacgcagc ttcccggcga gtatgacctt
     1561 tttgatttaa tggcgaaggt tactgaagat aacctgcacg ccccggtgga ttccgggcct
     1621 cctgtcggtc gggaagcgtt atagcttttt cgctggccag cgtatgtgta atacggtggt
     1681 attacatctt atttctttat tttcatgtaa ttacggttga ctgtaatacc ttgcgtatta
     1741 cacgtataaa cgaaaaatcc catttttccc atttgattca tgcagttgcg atgaaatcgc
     1801 gattgcgtat ggtgtatgac catttaaggg ataaagcaac ttggctttta aggcatgaat
     1861 ctatatctgg caggcctgag cgaaataaaa aagcgttaca tacctgccgg ttcatggcta
     1921 catgaaccgt gaaagacaag gataggacaa ttataagaca ttctgtgata ttttggacta
     1981 aaatgagaca ttgataagac attatgggtg gcgtatggcg aattttaacc ttggtccaag
     2041 aacagcgatt gcggctgtca gagattccct ggctgatata gaaaactgga agaaaaatgg
     2101 catccccagg agagaaattg tggctgtact gaatgaacgt tacggtctga agatctcaca
     2161 ggttgcgttt gataaggctc tttacaggtt gagaaaaaat acagatggat cgtctctcgc
     2221 tacagcggat tctttgcctg ctacagaaaa atctgtttct gtagcaggcg cgccagagaa
     2281 tggttttttt ctgtccgtga atgacttcag aagagtggaa gatgaatctc aaagactggc
     2341 tgagtcattg agggatagca ttggcaggag gaaggggttc tgatttccac tcgaaattgt
     2401 tttgtgaaac gttcgtacat ccgccccctt atcttcatgc ctgatgttct tgccaacgcc
     2461 tcacggccac gcaataaatt tcccgcccgt tcaccgtttt cggatgggaa gaacgccgga
     2521 aacaggactt accccggctg aatggcgtga atttccgcgc tatgcacttg cgcgcatact
     2581 catgcatgcc gtaaaaacag agcctgcgcg tttctggcgg gttttcgggt ggtttgttgc
     2641 ctgttttgcc ggtttcccgt cagaaacgcc ctgagggcct ctcaggtggt gcacgcaagg
     2701 gatgttatgt tcaatcgaaa tcagaaaaac gatcggtaaa gcgatcgttt ttctgatagc
     2761 atcatgttga ttttatataa cgtgggtgta aagaatgact agaccgattg ctgttgattt
     2821 atttgctgga gcgggtgggc tgagtctcgg tttcgagcaa gctggctttg atataatggc
     2881 atcagttgaa atagatccaa tacattgctc tgctcacaaa tataactttc ctatgtgcaa
     2941 aacgatatgt agaagtgttg ttgatgttac cggagaatac gttagggaag tttcaggtat
     3001 tggtgagaaa gagattgatg tagtgatcgg aggcgctccc tgccaaggct tttcattaat
     3061 aggaaaacgc gcgcttgatg atgatagaaa caaactggtc tatcactatg tacggctggt
     3121 tcttgagcta aagcctaaat actttatttt tgaaaatgta aaagggttga cggttggtaa
     3181 gcataagcag tttttagtag agataatgga tgcatttaaa gatggcgggt acgacgttgt
     3241 aagcgattat aaagtgctaa acgcagctga ttatggagtt cctcaagatc gccgtcgtct
     3301 tttcttaatg gggggaagga aaggaattgc tctgccatca taccctgagc cattatccat
     3361 tagaacaacg gttggggacg ctattgggga tattcctgat gcggaaaaat atcctgagct
     3421 atggggtaga gattgggttt atgctaaatt tggtgagcaa tcactatact catcctattt
     3481 gcatggcgta ggaaaagatc ctagtgattt tagctaccca aggattttta ataaagacaa
     3541 attaacgtgt tctttactga cagatcactc tgacatttct agagggcggt ttgttgaaac
     3601 tttgcctgac acggtagaac caatcagcag gtttaaaaag ctctcgatga atgggctatg
     3661 taatacttta agggcaggaa cagcaagtga cagaggtgct tttacatctc ctcgtcctat
     3721 acatccgatc tatcctaggg tcatcacggt cagagaggca gcaagactgc attcatatcc
     3781 tgattggttc agatttcatg tgactaagtg gcatggattt agacaggtcg gtaatagtgt
     3841 tcctcctatg ctagctagaa gtgttggctt gcagattatg aaggttcttg gtgttacgcc
     3901 aaaaaaacca acgaagaaaa tcaaactcgg tgatgaaagt ttggttgcta tttctatgtc
     3961 cgatgctgca tctatgtttg gtgtgtcatc aaatgtaatt gctaagagaa taaaaaatag
     4021 taacaaggag gttgtttgtg agtaaggata aaaaagaaag gtccaaaaat agataccatc
     4081 agttggtaga aaagatattt ttcgataaat atgttgatgg tgacttagag gttttgtttg
     4141 aaaggttaga gataaacagt gctgcaaaag atttaggtat agaactccca tctaatgttg
     4201 gtgatgttat atattcaatc agatttagaa cgcctatgcc agaaagtatt ctgttgactc
     4261 agccaga
//
