LOCUS       NZ_CP091629             4267 bp    DNA     circular CON 28-JAN-2024
DEFINITION  Salmonella enterica strain 1165 plasmid p1165-4, complete sequence.
ACCESSION   NZ_CP091629
VERSION     NZ_CP091629.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN25270674
            Assembly: GCF_026873445.1
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  JOURNAL   Unpublished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 13:46:28
            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)                     :: 4,720
            CDSs (total)                      :: 4,605
            Genes (coding)                    :: 4,480
            CDSs (with protein)               :: 4,480
            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)              :: 125
            CDSs (without protein)            :: 125
            Pseudo Genes (ambiguous residues) :: 0 of 125
            Pseudo Genes (frameshifted)       :: 47 of 125
            Pseudo Genes (incomplete)         :: 89 of 125
            Pseudo Genes (internal stop)      :: 28 of 125
            Pseudo Genes (multiple problems)  :: 36 of 125
            Pseudo Genes (short protein)      :: 1 of 125
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP091629.1.
            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="1165"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:28901"
                     /plasmid="p1165-4"
                     /geo_loc_name="China: Hangzhou"
                     /collection_date="2020-08"
                     /collected_by="Meina Yue"
     gene            join(4232..4267,1..333)
                     /locus_tag="L5507_RS23570"
                     /old_locus_tag="L5507_23580"
     CDS             join(4232..4267,1..333)
                     /locus_tag="L5507_RS23570"
                     /old_locus_tag="L5507_23580"
                     /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            745..1995
                     /locus_tag="L5507_RS23575"
                     /old_locus_tag="L5507_23585"
     CDS             745..1995
                     /locus_tag="L5507_RS23575"
                     /old_locus_tag="L5507_23585"
                     /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            1988..2797
                     /locus_tag="L5507_RS23580"
                     /old_locus_tag="L5507_23590"
     CDS             1988..2797
                     /locus_tag="L5507_RS23580"
                     /old_locus_tag="L5507_23590"
                     /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(3017..3148)
                     /locus_tag="L5507_RS23635"
     CDS             complement(3017..3148)
                     /locus_tag="L5507_RS23635"
                     /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            3712..3861
                     /locus_tag="L5507_RS23585"
                     /old_locus_tag="L5507_23595"
     CDS             3712..3861
                     /locus_tag="L5507_RS23585"
                     /old_locus_tag="L5507_23595"
                     /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"
     Typing          3503..3719
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.781"
                     /coverage="100.0"
                     /evalue="4.32e-80"
     Typing          complement(3040..3520)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.925"
                     /coverage="92.0"
                     /evalue="0.0"
ORIGIN
        1 gcggctgtca gagattccct ggctgatata gaaaactgga agaaaaatgg catccccagg
       61 agagaaattg tggctgtact gaatgaacgt tacggtctga agatctcaca ggttgcgttt
      121 gataaggctc tttacaggtt gagaaaaaat acagatggat cgtctctcgc tacagcggat
      181 tctttgcctg ctacagaaaa atctgtttct gtagcaggcg cgccagagaa tggttttttt
      241 ctgtccgtga atgacttcag aagagtggaa gatgaatctc aaagactggc tgagtcattg
      301 agggatagca ttggcaggag gaaggggttc tgatttccac tcgaaattgt tttgtgaaac
      361 gttcgtacat ccgccccctt atcttcatgc ctgatgttct tgccaacgcc tcacggccac
      421 gcaataaatt tcccgcccgt tcaccgtttt cggatgggaa gaacgccgga aacaggactt
      481 accccggctg aatggcgtga atttccgcgc tatgcacttg cgcgcatact catgcatgcc
      541 gtaaaaacag agcctgcgcg tttctggcgg gttttcgggt ggtttgttgc ctgttttgcc
      601 ggtttcccgt cagaaacgcc ctgagggcct ctcaggtggt gcacgcaagg gatgttatgt
      661 tcaatcgaaa tcagaaaaac gatcggtaaa gcgatcgttt ttctgatagc atcatgttga
      721 ttttatataa cgtgggtgta aagaatgact agaccgattg ctgttgattt atttgctgga
      781 gcgggtgggc tgagtctcgg tttcgagcaa gctggctttg atataatggc atcagttgaa
      841 atagatccaa tacattgctc tgctcacaaa tataactttc ctatgtgcaa aacgatatgt
      901 agaagtgttg ttgatgttac cggagaatac gttagggaag tttcaggtat tggtgagaaa
      961 gagattgatg tagtgatcgg aggcgctccc tgccaaggct tttcattaat aggaaaacgc
     1021 gcgcttgatg atgatagaaa caaactggtc tatcactatg tacggctggt tcttgagcta
     1081 aagcctaaat actttatttt tgaaaatgta aaagggttga cggttggtaa gcataagcag
     1141 tttttagtag agataatgga tgcatttaaa gatggcgggt acgacgttgt aagcgattat
     1201 aaagtgctaa acgcagctga ttatggagtt cctcaagatc gccgtcgtct tttcttaatg
     1261 gggggaagga aaggaattgc tctgccatca taccctgagc cattatccat tagaacaacg
     1321 gttggggacg ctattgggga tattcctgat gcggaaaaat atcctgagct atggggtaga
     1381 gattgggttt atgctaaatt tggtgagcaa tcactatact catcctattt gcatggcgta
     1441 ggaaaagatc ctagtgattt tagctaccca aggattttta ataaagacaa attaacgtgt
     1501 tctttactga cagatcactc tgacatttct agagggcggt ttgttgaaac tttgcctgac
     1561 acggtagaac caatcagcag gtttaaaaag ctctcgatga atgggctatg taatacttta
     1621 agggcaggaa cagcaagtga cagaggtgct tttacatctc ctcgtcctat acatccgatc
     1681 tatcctaggg tcatcacggt cagagaggca gcaagactgc attcatatcc tgattggttc
     1741 agatttcatg tgactaagtg gcatggattt agacaggtcg gtaatagtgt tcctcctatg
     1801 ctagctagaa gtgttggctt gcagattatg aaggttcttg gtgttacgcc aaaaaaacca
     1861 acgaagaaaa tcaaactcgg tgatgaaagt ttggttgcta tttctatgtc cgatgctgca
     1921 tctatgtttg gtgtgtcatc aaatgtaatt gctaagagaa taaaaaatag taacaaggag
     1981 gttgtttgtg agtaaggata aaaaagaaag gtccaaaaat agataccatc agttggtaga
     2041 aaagatattt ttcgataaat atgttgatgg tgacttagag gttttgtttg aaaggttaga
     2101 gataaacagt gctgcaaaag atttaggtat agaactccca tctaatgttg gtgatgttat
     2161 atattcaatc agatttagaa cgcctatgcc agaaagtatt ctgttgactc agccagaagg
     2221 taaggagtgg attattgagc tggctggtag gtcaaagtat cgatttagat tagtaactat
     2281 tagtaggatt ttgccaaatc ctaatatggt ggcaataaaa attccagaca ataccccgga
     2341 gataattaca ggttattctt tagacgacga gcaggcattg ctggcgaagg tgagatataa
     2401 ccggctaata gatatatttc taggtataac cacatattct ttacagaatc atttaagaac
     2461 tacggtgaag ggaattggtc aaatagagat cgatgaactt tatgtaggta tagataaata
     2521 cggttgccat tatataatac cagttcaagc aaaaggtggg acagatcaaa tatcaatggt
     2581 gcaaacatcg caagatacag cgtggtgtga acaaaaatac ccaaatgtta gatgtagagc
     2641 tatttccgct cagtttgttt cgagcgattt gattgcactg tttgagctaa agatagacga
     2701 aggacaagtg aaattgattg aggaaaggca ttacaaactg gttccggcaa aagagttaga
     2761 tagctctgac atctcaaact accgcatgtc tgtataattt ctgagaggat cttcttgaga
     2821 tcctttcgtt ctagccgtaa tctcctaagc cgtaaacaaa aaaaccaccg ctaccaacgg
     2881 tggttcgttt gccggaattt agagctacca actctttctt ccgaaggtaa ctggctttca
     2941 cggagcgcag ataccaaaac tgtcctttca gtgtagccgt agtcaggcca ccacttcaag
     3001 aactctgtag ataactctac tccgctccgt gaatccgatt accagtggct gctgccagtg
     3061 gcgcttttgc atgtctttcc gggttggact caagacgata gttaccggac aaggcgcagc
     3121 agtcggactg aacggggggt tcgtgcatac agtccagctt ggagcgaact gcctacccgg
     3181 aactgagtgt caggcgtgga atgagacaaa cgcggccata acagcggaat gacaccggta
     3241 aaccgaaagg caggaacagg agagcgcacg agggagctac cagggggaaa cgcctgggat
     3301 ctttatagtc ctgtcgggtt tcgccaccac tgatttgagc gtcagatttt gtgatgcttg
     3361 tcaggggggc ggagcctatg gaaaaacggc aacgccgcat cctttttcct gactttcctg
     3421 acttgagcgc aatctcgtta tctcgtcctt cgtgagctgg taacgcccgc cgcagtctca
     3481 cggcaggagc gcagcgaccg agtgagcgag gaggcgtcat ttcatcgtta cctgcatttt
     3541 gcacttacgc cccgcagccg tattttcccc cttgccacat gaagcacttc cccgaatctc
     3601 catctcgccg taacatacta agccagtata cactccgcta gcgctacgtg actggttcag
     3661 ggctgcgccc cgaaacccgc taacaacctc tcagctactg gatatcaccc catgccatct
     3721 gaacatgatg aacaacggga tgctgctgat acgcagcttc ccggcgagta tgaccttttt
     3781 gatttaatgg cgaaggttac tgaagataac ctgcacgccc cggtggattc cgggcctcct
     3841 gtcggtcggg aagcgttata gctttttcgc tggccagcgt atgtgtaata cggtggtatt
     3901 acatcttatt tctttatttt catgtaatta cggttgactg taataccttg cgtattacac
     3961 gtataaacga aaaatcccat ttttcccatt tgattcatgc agttgcgatg aaatcgcgat
     4021 tgcgtatggt gtatgaccat ttaagggata aagcaacttg gcttttaagg catgaatcta
     4081 tatctggcag gcctgagcga aataaaaaag cgttacatac ctgccggttc atggctacat
     4141 gaaccgtgaa agacaaggat aggacaatta taagacattc tgtgatattt tggactaaaa
     4201 tgagacattg ataagacatt atgggtggcg tatggcgaat tttaaccttg gtccaagaac
     4261 agcgatt
//
