LOCUS       NZ_CP060854             4267 bp    DNA     circular CON 24-MAY-2024
DEFINITION  Salmonella enterica strain 467 plasmid p467-3, complete sequence.
ACCESSION   NZ_CP060854
VERSION     NZ_CP060854.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15941596
            Assembly: GCF_022559465.1
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  JOURNAL   Unpublished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_022559465.1-RS_2024_05_24
            Annotation Date                   :: 05/24/2024 04:15:24
            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)                     :: 4,789
            CDSs (total)                      :: 4,674
            Genes (coding)                    :: 4,541
            CDSs (with protein)               :: 4,541
            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)              :: 133
            CDSs (without protein)            :: 133
            Pseudo Genes (ambiguous residues) :: 0 of 133
            Pseudo Genes (frameshifted)       :: 48 of 133
            Pseudo Genes (incomplete)         :: 98 of 133
            Pseudo Genes (internal stop)      :: 29 of 133
            Pseudo Genes (multiple problems)  :: 38 of 133
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP060854.1.
            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="467"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:28901"
                     /plasmid="p467-3"
                     /geo_loc_name="China: Hangzhou"
                     /collection_date="2018-07"
                     /collected_by="Meina Yue"
     gene            195..344
                     /locus_tag="IAR30_RS23930"
                     /old_locus_tag="IAR30_23760"
     CDS             195..344
                     /locus_tag="IAR30_RS23930"
                     /old_locus_tag="IAR30_23760"
                     /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            715..1083
                     /locus_tag="IAR30_RS23935"
                     /old_locus_tag="IAR30_23765"
     CDS             715..1083
                     /locus_tag="IAR30_RS23935"
                     /old_locus_tag="IAR30_23765"
                     /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            1495..2745
                     /locus_tag="IAR30_RS23940"
                     /old_locus_tag="IAR30_23770"
     CDS             1495..2745
                     /locus_tag="IAR30_RS23940"
                     /old_locus_tag="IAR30_23770"
                     /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            2738..3547
                     /locus_tag="IAR30_RS23945"
                     /old_locus_tag="IAR30_23775"
     CDS             2738..3547
                     /locus_tag="IAR30_RS23945"
                     /old_locus_tag="IAR30_23775"
                     /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(3767..3898)
                     /locus_tag="IAR30_RS24020"
     CDS             complement(3767..3898)
                     /locus_tag="IAR30_RS24020"
                     /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          2..202
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.133"
                     /coverage="93.0"
                     /evalue="3.38e-71"
     Typing          complement(3790..4267)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.875"
                     /coverage="92.0"
                     /evalue="0.0"
ORIGIN
        1 catttcatcg ttacctgcat tttgcactta cgccccgcag ccgtattttc ccccttgcca
       61 catgaagcac ttccccgaat ctccatctcg ccgtaacata ctaagccagt atacactccg
      121 ctagcgctac gtgactggtt cagggctgcg ccccgaaacc cgctaacaac ctctcagcta
      181 ctggatatca ccccatgcca tctgaacatg atgaacaacg ggatgctgct gatacgcagc
      241 ttcccggcga gtatgacctt tttgatttaa tggcgaaggt tactgaagat aacctgcacg
      301 ccccggtgga ttccgggcct cctgtcggtc gggaagcgtt atagcttttt cgctggccag
      361 cgtatgtgta atacggtggt attacatctt atttctttat tttcatgtaa ttacggttga
      421 ctgtaatacc ttgcgtatta cacgtataaa cgaaaaatcc catttttccc atttgattca
      481 tgcagttgcg atgaaatcgc gattgcgtat ggtgtatgac catttaaggg ataaagcaac
      541 ttggctttta aggcatgaat ctatatctgg caggcctgag cgaaataaaa aagcgttaca
      601 tacctgccgg ttcatggcta catgaaccgt gaaagacaag gataggacaa ttataagaca
      661 ttctgtgata ttttggacta aaatgagaca ttgataagac attatgggtg gcgtatggcg
      721 aattttaacc ttggtccaag aacagcgatt gcggctgtca gagattccct ggctgatata
      781 gaaaactgga agaaaaatgg catccccagg agagaaattg tggctgtact gaatgaacgt
      841 tacggtctga agatctcaca ggttgcgttt gataaggctc tttacaggtt gagaaaaaat
      901 acagatggat cgtctctcgc tacagcggat tctttgcctg ctacagaaaa atctgtttct
      961 gtagcaggcg cgccagagaa tggttttttt ctgtccgtga atgacttcag aagagtggaa
     1021 gatgaatctc aaagactggc tgagtcattg agggatagca ttggcaggag gaaggggttc
     1081 tgatttccac tcgaaattgt tttgtgaaac gttcgtacat ccgccccctt atcttcatgc
     1141 ctgatgttct tgccaacgcc tcacggccac gcaataaatt tcccgcccgt tcaccgtttt
     1201 cggatgggaa gaacgccgga aacaggactt accccggctg aatggcgtga atttccgcgc
     1261 tatgcacttg cgcgcatact catgcatgcc gtaaaaacag agcctgcgcg tttctggcgg
     1321 gttttcgggt ggtttgttgc ctgttttgcc ggtttcccgt cagaaacgcc ctgagggcct
     1381 ctcaggtggt gcacgcaagg gatgttatgt tcaatcgaaa tcagaaaaac gatcggtaaa
     1441 gcgatcgttt ttctgatagc atcatgttga ttttatataa cgtgggtgta aagaatgact
     1501 agaccgattg ctgttgattt atttgctgga gcgggtgggc tgagtctcgg tttcgagcaa
     1561 gctggctttg atataatggc atcagttgaa atagatccaa tacattgctc tgctcacaaa
     1621 tataactttc ctatgtgcaa aacgatatgt agaagtgttg ttgatgttac cggagaatac
     1681 gttagggaag tttcaggtat tggtgagaaa gagattgatg tagtgatcgg aggcgctccc
     1741 tgccaaggct tttcattaat aggaaaacgc gcgcttgatg atgatagaaa caaactggtc
     1801 tatcactatg tacggctggt tcttgagcta aagcctaaat actttatttt tgaaaatgta
     1861 aaagggttga cggttggtaa gcataagcag tttttagtag agataatgga tgcatttaaa
     1921 gatggcgggt acgacgttgt aagcgattat aaagtgctaa acgcagctga ttatggagtt
     1981 cctcaagatc gccgtcgtct tttcttaatg gggggaagga aaggaattgc tctgccatca
     2041 taccctgagc cattatccat tagaacaacg gttggggacg ctattgggga tattcctgat
     2101 gcggaaaaat atcctgagct atggggtaga gattgggttt atgctaaatt tggtgagcaa
     2161 tcactatact catcctattt gcatggcgta ggaaaagatc ctagtgattt tagctaccca
     2221 aggattttta ataaagacaa attaacgtgt tctttactga cagatcactc tgacatttct
     2281 agagggcggt ttgttgaaac tttgcctgac acggtagaac caatcagcag gtttaaaaag
     2341 ctctcgatga atgggctatg taatacttta agggcaggaa cagcaagtga cagaggtgct
     2401 tttacatctc ctcgtcctat acatccgatc tatcctaggg tcatcacggt cagagaggca
     2461 gcaagactgc attcatatcc tgattggttc agatttcatg tgactaagtg gcatggattt
     2521 agacaggtcg gtaatagtgt tcctcctatg ctagctagaa gtgttggctt gcagattatg
     2581 aaggttcttg gtgttacgcc aaaaaaacca acgaagaaaa tcaaactcgg tgatgaaagt
     2641 ttggttgcta tttctatgtc cgatgctgca tctatgtttg gtgtgtcatc aaatgtaatt
     2701 gctaagagaa taaaaaatag taacaaggag gttgtttgtg agtaaggata aaaaagaaag
     2761 gtccaaaaat agataccatc agttggtaga aaagatattt ttcgataaat atgttgatgg
     2821 tgacttagag gttttgtttg aaaggttaga gataaacagt gctgcaaaag atttaggtat
     2881 agaactccca tctaatgttg gtgatgttat atattcaatc agatttagaa cgcctatgcc
     2941 agaaagtatt ctgttgactc agccagaagg taaggagtgg attattgagc tggctggtag
     3001 gtcaaagtat cgatttagat tagtaactat tagtaggatt ttgccaaatc ctaatatggt
     3061 ggcaataaaa attccagaca ataccccgga gataattaca ggttattctt tagacgacga
     3121 gcaggcattg ctggcgaagg tgagatataa ccggctaata gatatatttc taggtataac
     3181 cacatattct ttacagaatc atttaagaac tacggtgaag ggaattggtc aaatagagat
     3241 cgatgaactt tatgtaggta tagataaata cggttgccat tatataatac cagttcaagc
     3301 aaaaggtggg acagatcaaa tatcaatggt gcaaacatcg caagatacag cgtggtgtga
     3361 acaaaaatac ccaaatgtta gatgtagagc tatttccgct cagtttgttt cgagcgattt
     3421 gattgcactg tttgagctaa agatagacga aggacaagtg aaattgattg aggaaaggca
     3481 ttacaaactg gttccggcaa aagagttaga tagctctgac atctcaaact accgcatgtc
     3541 tgtataattt ctgagaggat cttcttgaga tcctttcgtt ctagccgtaa tctcctaagc
     3601 cgtaaacaaa aaaaccaccg ctaccaacgg tggttcgttt gccggaattt agagctacca
     3661 actctttctt ccgaaggtaa ctggctttca cggagcgcag ataccaaaac tgtcctttca
     3721 gtgtagccgt agtcaggcca ccacttcaag aactctgtag ataactctac tccgctccgt
     3781 gaatccgatt accagtggct gctgccagtg gcgcttttgc atgtctttcc gggttggact
     3841 caagacgata gttaccggac aaggcgcagc agtcggactg aacggggggt tcgtgcatac
     3901 agtccagctt ggagcgaact gcctacccgg aactgagtgt caggcgtgga atgagacaaa
     3961 cgcggccata acagcggaat gacaccggta aaccgaaagg caggaacagg agagcgcacg
     4021 agggagctac cagggggaaa cgcctgggat ctttatagtc ctgtcgggtt tcgccaccac
     4081 tgatttgagc gtcagatttt gtgatgcttg tcaggggggc ggagcctatg gaaaaacggc
     4141 aacgccgcat cctttttcct gactttcctg acttgagcgc aatctcgtta tctcgtcctt
     4201 cgtgagctgg taacgcccgc cgcagtctca cggcaggagc gcagcgaccg agtgagcgag
     4261 gaggcgt
//
