LOCUS       NZ_CP091606             4267 bp    DNA     circular CON 28-JAN-2024
DEFINITION  Salmonella enterica strain 1902 plasmid p1902-2, complete sequence.
ACCESSION   NZ_CP091606
VERSION     NZ_CP091606.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN25270681
            Assembly: GCF_026873305.1
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  JOURNAL   Unpublished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)                     :: 4,767
            CDSs (total)                      :: 4,652
            Genes (coding)                    :: 4,523
            CDSs (with protein)               :: 4,523
            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)       :: 47 of 129
            Pseudo Genes (incomplete)         :: 93 of 129
            Pseudo Genes (internal stop)      :: 29 of 129
            Pseudo Genes (multiple problems)  :: 37 of 129
            Pseudo Genes (short protein)      :: 1 of 129
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP091606.1.
            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="1902"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:28901"
                     /plasmid="p1902-2"
                     /geo_loc_name="China: Hangzhou"
                     /collection_date="2021-09"
                     /collected_by="Meina Yue"
     gene            join(3659..4267,1..201)
                     /locus_tag="L5514_RS23810"
                     /old_locus_tag="L5514_23825"
     CDS             join(3659..4267,1..201)
                     /locus_tag="L5514_RS23810"
                     /old_locus_tag="L5514_23825"
                     /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(421..552)
                     /locus_tag="L5514_RS23870"
     CDS             complement(421..552)
                     /locus_tag="L5514_RS23870"
                     /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            1116..1265
                     /locus_tag="L5514_RS23815"
                     /old_locus_tag="L5514_23830"
     CDS             1116..1265
                     /locus_tag="L5514_RS23815"
                     /old_locus_tag="L5514_23830"
                     /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            1636..2004
                     /locus_tag="L5514_RS23820"
                     /old_locus_tag="L5514_23835"
     CDS             1636..2004
                     /locus_tag="L5514_RS23820"
                     /old_locus_tag="L5514_23835"
                     /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            2416..3666
                     /locus_tag="L5514_RS23825"
                     /old_locus_tag="L5514_23840"
     CDS             2416..3666
                     /locus_tag="L5514_RS23825"
                     /old_locus_tag="L5514_23840"
                     /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          907..1123
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.781"
                     /coverage="100.0"
                     /evalue="4.32e-80"
     Typing          complement(444..924)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.925"
                     /coverage="92.0"
                     /evalue="0.0"
ORIGIN
        1 acagcgtggt gtgaacaaaa atacccaaat gttagatgta gagctatttc cgctcagttt
       61 gtttcgagcg atttgattgc actgtttgag ctaaagatag acgaaggaca agtgaaattg
      121 attgaggaaa ggcattacaa actggttccg gcaaaagagt tagatagctc tgacatctca
      181 aactaccgca tgtctgtata atttctgaga ggatcttctt gagatccttt cgttctagcc
      241 gtaatctcct aagccgtaaa caaaaaaacc accgctacca acggtggttc gtttgccgga
      301 atttagagct accaactctt tcttccgaag gtaactggct ttcacggagc gcagatacca
      361 aaactgtcct ttcagtgtag ccgtagtcag gccaccactt caagaactct gtagataact
      421 ctactccgct ccgtgaatcc gattaccagt ggctgctgcc agtggcgctt ttgcatgtct
      481 ttccgggttg gactcaagac gatagttacc ggacaaggcg cagcagtcgg actgaacggg
      541 gggttcgtgc atacagtcca gcttggagcg aactgcctac ccggaactga gtgtcaggcg
      601 tggaatgaga caaacgcggc cataacagcg gaatgacacc ggtaaaccga aaggcaggaa
      661 caggagagcg cacgagggag ctaccagggg gaaacgcctg ggatctttat agtcctgtcg
      721 ggtttcgcca ccactgattt gagcgtcaga ttttgtgatg cttgtcaggg gggcggagcc
      781 tatggaaaaa cggcaacgcc gcatcctttt tcctgacttt cctgacttga gcgcaatctc
      841 gttatctcgt ccttcgtgag ctggtaacgc ccgccgcagt ctcacggcag gagcgcagcg
      901 accgagtgag cgaggaggcg tcatttcatc gttacctgca ttttgcactt acgccccgca
      961 gccgtatttt cccccttgcc acatgaagca cttccccgaa tctccatctc gccgtaacat
     1021 actaagccag tatacactcc gctagcgcta cgtgactggt tcagggctgc gccccgaaac
     1081 ccgctaacaa cctctcagct actggatatc accccatgcc atctgaacat gatgaacaac
     1141 gggatgctgc tgatacgcag cttcccggcg agtatgacct ttttgattta atggcgaagg
     1201 ttactgaaga taacctgcac gccccggtgg attccgggcc tcctgtcggt cgggaagcgt
     1261 tatagctttt tcgctggcca gcgtatgtgt aatacggtgg tattacatct tatttcttta
     1321 ttttcatgta attacggttg actgtaatac cttgcgtatt acacgtataa acgaaaaatc
     1381 ccatttttcc catttgattc atgcagttgc gatgaaatcg cgattgcgta tggtgtatga
     1441 ccatttaagg gataaagcaa cttggctttt aaggcatgaa tctatatctg gcaggcctga
     1501 gcgaaataaa aaagcgttac atacctgccg gttcatggct acatgaaccg tgaaagacaa
     1561 ggataggaca attataagac attctgtgat attttggact aaaatgagac attgataaga
     1621 cattatgggt ggcgtatggc gaattttaac cttggtccaa gaacagcgat tgcggctgtc
     1681 agagattccc tggctgatat agaaaactgg aagaaaaatg gcatccccag gagagaaatt
     1741 gtggctgtac tgaatgaacg ttacggtctg aagatctcac aggttgcgtt tgataaggct
     1801 ctttacaggt tgagaaaaaa tacagatgga tcgtctctcg ctacagcgga ttctttgcct
     1861 gctacagaaa aatctgtttc tgtagcaggc gcgccagaga atggtttttt tctgtccgtg
     1921 aatgacttca gaagagtgga agatgaatct caaagactgg ctgagtcatt gagggatagc
     1981 attggcagga ggaaggggtt ctgatttcca ctcgaaattg ttttgtgaaa cgttcgtaca
     2041 tccgccccct tatcttcatg cctgatgttc ttgccaacgc ctcacggcca cgcaataaat
     2101 ttcccgcccg ttcaccgttt tcggatggga agaacgccgg aaacaggact taccccggct
     2161 gaatggcgtg aatttccgcg ctatgcactt gcgcgcatac tcatgcatgc cgtaaaaaca
     2221 gagcctgcgc gtttctggcg ggttttcggg tggtttgttg cctgttttgc cggtttcccg
     2281 tcagaaacgc cctgagggcc tctcaggtgg tgcacgcaag ggatgttatg ttcaatcgaa
     2341 atcagaaaaa cgatcggtaa agcgatcgtt tttctgatag catcatgttg attttatata
     2401 acgtgggtgt aaagaatgac tagaccgatt gctgttgatt tatttgctgg agcgggtggg
     2461 ctgagtctcg gtttcgagca agctggcttt gatataatgg catcagttga aatagatcca
     2521 atacattgct ctgctcacaa atataacttt cctatgtgca aaacgatatg tagaagtgtt
     2581 gttgatgtta ccggagaata cgttagggaa gtttcaggta ttggtgagaa agagattgat
     2641 gtagtgatcg gaggcgctcc ctgccaaggc ttttcattaa taggaaaacg cgcgcttgat
     2701 gatgatagaa acaaactggt ctatcactat gtacggctgg ttcttgagct aaagcctaaa
     2761 tactttattt ttgaaaatgt aaaagggttg acggttggta agcataagca gtttttagta
     2821 gagataatgg atgcatttaa agatggcggg tacgacgttg taagcgatta taaagtgcta
     2881 aacgcagctg attatggagt tcctcaagat cgccgtcgtc ttttcttaat ggggggaagg
     2941 aaaggaattg ctctgccatc ataccctgag ccattatcca ttagaacaac ggttggggac
     3001 gctattgggg atattcctga tgcggaaaaa tatcctgagc tatggggtag agattgggtt
     3061 tatgctaaat ttggtgagca atcactatac tcatcctatt tgcatggcgt aggaaaagat
     3121 cctagtgatt ttagctaccc aaggattttt aataaagaca aattaacgtg ttctttactg
     3181 acagatcact ctgacatttc tagagggcgg tttgttgaaa ctttgcctga cacggtagaa
     3241 ccaatcagca ggtttaaaaa gctctcgatg aatgggctat gtaatacttt aagggcagga
     3301 acagcaagtg acagaggtgc ttttacatct cctcgtccta tacatccgat ctatcctagg
     3361 gtcatcacgg tcagagaggc agcaagactg cattcatatc ctgattggtt cagatttcat
     3421 gtgactaagt ggcatggatt tagacaggtc ggtaatagtg ttcctcctat gctagctaga
     3481 agtgttggct tgcagattat gaaggttctt ggtgttacgc caaaaaaacc aacgaagaaa
     3541 atcaaactcg gtgatgaaag tttggttgct atttctatgt ccgatgctgc atctatgttt
     3601 ggtgtgtcat caaatgtaat tgctaagaga ataaaaaata gtaacaagga ggttgtttgt
     3661 gagtaaggat aaaaaagaaa ggtccaaaaa tagataccat cagttggtag aaaagatatt
     3721 tttcgataaa tatgttgatg gtgacttaga ggttttgttt gaaaggttag agataaacag
     3781 tgctgcaaaa gatttaggta tagaactccc atctaatgtt ggtgatgtta tatattcaat
     3841 cagatttaga acgcctatgc cagaaagtat tctgttgact cagccagaag gtaaggagtg
     3901 gattattgag ctggctggta ggtcaaagta tcgatttaga ttagtaacta ttagtaggat
     3961 tttgccaaat cctaatatgg tggcaataaa aattccagac aataccccgg agataattac
     4021 aggttattct ttagacgacg agcaggcatt gctggcgaag gtgagatata accggctaat
     4081 agatatattt ctaggtataa ccacatattc tttacagaat catttaagaa ctacggtgaa
     4141 gggaattggt caaatagaga tcgatgaact ttatgtaggt atagataaat acggttgcca
     4201 ttatataata ccagttcaag caaaaggtgg gacagatcaa atatcaatgg tgcaaacatc
     4261 gcaagat
//
