LOCUS       NZ_CP091635             4267 bp    DNA     circular CON 28-JAN-2024
DEFINITION  Salmonella enterica strain 1116 plasmid p1116-1, complete sequence.
ACCESSION   NZ_CP091635
VERSION     NZ_CP091635.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN25270672
            Assembly: GCF_026873485.1
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  JOURNAL   Unpublished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 13:38:40
            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)                     :: 4,494
            CDSs (total)                      :: 4,379
            Genes (coding)                    :: 4,277
            CDSs (with protein)               :: 4,277
            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)              :: 102
            CDSs (without protein)            :: 102
            Pseudo Genes (ambiguous residues) :: 0 of 102
            Pseudo Genes (frameshifted)       :: 42 of 102
            Pseudo Genes (incomplete)         :: 70 of 102
            Pseudo Genes (internal stop)      :: 26 of 102
            Pseudo Genes (multiple problems)  :: 34 of 102
            Pseudo Genes (short protein)      :: 1 of 102
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP091635.1.
            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="1116"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:28901"
                     /plasmid="p1116-1"
                     /geo_loc_name="China: Hangzhou"
                     /collection_date="2020-08"
                     /collected_by="Meina Yue"
     gene            complement(join(4209..4267,1..751))
                     /locus_tag="L5505_RS22445"
                     /old_locus_tag="L5505_22460"
     CDS             complement(join(4209..4267,1..751))
                     /locus_tag="L5505_RS22445"
                     /old_locus_tag="L5505_22460"
                     /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(744..1994)
                     /locus_tag="L5505_RS22450"
                     /old_locus_tag="L5505_22465"
     CDS             complement(744..1994)
                     /locus_tag="L5505_RS22450"
                     /old_locus_tag="L5505_22465"
                     /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            complement(2406..2774)
                     /locus_tag="L5505_RS22455"
                     /old_locus_tag="L5505_22470"
     CDS             complement(2406..2774)
                     /locus_tag="L5505_RS22455"
                     /old_locus_tag="L5505_22470"
                     /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            complement(3145..3294)
                     /locus_tag="L5505_RS22460"
                     /old_locus_tag="L5505_22475"
     CDS             complement(3145..3294)
                     /locus_tag="L5505_RS22460"
                     /old_locus_tag="L5505_22475"
                     /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            3858..3989
                     /locus_tag="L5505_RS22505"
     CDS             3858..3989
                     /locus_tag="L5505_RS22505"
                     /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          complement(3288..3504)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.781"
                     /coverage="100.0"
                     /evalue="4.32e-80"
     Typing          3451..3967
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.192"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gtttgtaatg cctttcctca atcaatttca cttgtccttc gtctatcttt agctcaaaca
       61 gtgcaatcaa atcgctcgaa acaaactgag cggaaatagc tctacatcta acatttgggt
      121 atttttgttc acaccacgct gtatcttgcg atgtttgcac cattgatatt tgatctgtcc
      181 caccttttgc ttgaactggt attatataat ggcaaccgta tttatctata cctacataaa
      241 gttcatcgat ctctatttga ccaattccct tcaccgtagt tcttaaatga ttctgtaaag
      301 aatatgtggt tatacctaga aatatatcta ttagccggtt atatctcacc ttcgccagca
      361 atgcctgctc gtcgtctaaa gaataacctg taattatctc cggggtattg tctggaattt
      421 ttattgccac catattagga tttggcaaaa tcctactaat agttactaat ctaaatcgat
      481 actttgacct accagccagc tcaataatcc actccttacc ttctggctga gtcaacagaa
      541 tactttctgg cataggcgtt ctaaatctga ttgaatatat aacatcacca acattagatg
      601 ggagttctat acctaaatct tttgcagcac tgtttatctc taacctttca aacaaaacct
      661 ctaagtcacc atcaacatat ttatcgaaaa atatcttttc taccaactga tggtatctat
      721 ttttggacct ttctttttta tccttactca caaacaacct ccttgttact attttttatt
      781 ctcttagcaa ttacatttga tgacacacca aacatagatg cagcatcgga catagaaata
      841 gcaaccaaac tttcatcacc gagtttgatt ttcttcgttg gtttttttgg cgtaacacca
      901 agaaccttca taatctgcaa gccaacactt ctagctagca taggaggaac actattaccg
      961 acctgtctaa atccatgcca cttagtcaca tgaaatctga accaatcagg atatgaatgc
     1021 agtcttgctg cctctctgac cgtgatgacc ctaggataga tcggatgtat aggacgagga
     1081 gatgtaaaag cacctctgtc acttgctgtt cctgccctta aagtattaca tagcccattc
     1141 atcgagagct ttttaaacct gctgattggt tctaccgtgt caggcaaagt ttcaacaaac
     1201 cgccctctag aaatgtcaga gtgatctgtc agtaaagaac acgttaattt gtctttatta
     1261 aaaatccttg ggtagctaaa atcactagga tcttttccta cgccatgcaa ataggatgag
     1321 tatagtgatt gctcaccaaa tttagcataa acccaatctc taccccatag ctcaggatat
     1381 ttttccgcat caggaatatc cccaatagcg tccccaaccg ttgttctaat ggataatggc
     1441 tcagggtatg atggcagagc aattcctttc cttcccccca ttaagaaaag acgacggcga
     1501 tcttgaggaa ctccataatc agctgcgttt agcactttat aatcgcttac aacgtcgtac
     1561 ccgccatctt taaatgcatc cattatctct actaaaaact gcttatgctt accaaccgtc
     1621 aaccctttta cattttcaaa aataaagtat ttaggcttta gctcaagaac cagccgtaca
     1681 tagtgataga ccagtttgtt tctatcatca tcaagcgcgc gttttcctat taatgaaaag
     1741 ccttggcagg gagcgcctcc gatcactaca tcaatctctt tctcaccaat acctgaaact
     1801 tccctaacgt attctccggt aacatcaaca acacttctac atatcgtttt gcacatagga
     1861 aagttatatt tgtgagcaga gcaatgtatt ggatctattt caactgatgc cattatatca
     1921 aagccagctt gctcgaaacc gagactcagc ccacccgctc cagcaaataa atcaacagca
     1981 atcggtctag tcattcttta cacccacgtt atataaaatc aacatgatgc tatcagaaaa
     2041 acgatcgctt taccgatcgt ttttctgatt tcgattgaac ataacatccc ttgcgtgcac
     2101 cacctgagag gccctcaggg cgtttctgac gggaaaccgg caaaacaggc aacaaaccac
     2161 ccgaaaaccc gccagaaacg cgcaggctct gtttttacgg catgcatgag tatgcgcgca
     2221 agtgcatagc gcggaaattc acgccattca gccggggtaa gtcctgtttc cggcgttctt
     2281 cccatccgaa aacggtgaac gggcgggaaa tttattgcgt ggccgtgagg cgttggcaag
     2341 aacatcaggc atgaagataa gggggcggat gtacgaacgt ttcacaaaac aatttcgagt
     2401 ggaaatcaga accccttcct cctgccaatg ctatccctca atgactcagc cagtctttga
     2461 gattcatctt ccactcttct gaagtcattc acggacagaa aaaaaccatt ctctggcgcg
     2521 cctgctacag aaacagattt ttctgtagca ggcaaagaat ccgctgtagc gagagacgat
     2581 ccatctgtat tttttctcaa cctgtaaaga gccttatcaa acgcaacctg tgagatcttc
     2641 agaccgtaac gttcattcag tacagccaca atttctctcc tggggatgcc atttttcttc
     2701 cagttttcta tatcagccag ggaatctctg acagccgcaa tcgctgttct tggaccaagg
     2761 ttaaaattcg ccatacgcca cccataatgt cttatcaatg tctcatttta gtccaaaata
     2821 tcacagaatg tcttataatt gtcctatcct tgtctttcac ggttcatgta gccatgaacc
     2881 ggcaggtatg taacgctttt ttatttcgct caggcctgcc agatatagat tcatgcctta
     2941 aaagccaagt tgctttatcc cttaaatggt catacaccat acgcaatcgc gatttcatcg
     3001 caactgcatg aatcaaatgg gaaaaatggg atttttcgtt tatacgtgta atacgcaagg
     3061 tattacagtc aaccgtaatt acatgaaaat aaagaaataa gatgtaatac caccgtatta
     3121 cacatacgct ggccagcgaa aaagctataa cgcttcccga ccgacaggag gcccggaatc
     3181 caccggggcg tgcaggttat cttcagtaac cttcgccatt aaatcaaaaa ggtcatactc
     3241 gccgggaagc tgcgtatcag cagcatcccg ttgttcatca tgttcagatg gcatggggtg
     3301 atatccagta gctgagaggt tgttagcggg tttcggggcg cagccctgaa ccagtcacgt
     3361 agcgctagcg gagtgtatac tggcttagta tgttacggcg agatggagat tcggggaagt
     3421 gcttcatgtg gcaaggggga aaatacggct gcggggcgta agtgcaaaat gcaggtaacg
     3481 atgaaatgac gcctcctcgc tcactcggtc gctgcgctcc tgccgtgaga ctgcggcggg
     3541 cgttaccagc tcacgaagga cgagataacg agattgcgct caagtcagga aagtcaggaa
     3601 aaaggatgcg gcgttgccgt ttttccatag gctccgcccc cctgacaagc atcacaaaat
     3661 ctgacgctca aatcagtggt ggcgaaaccc gacaggacta taaagatccc aggcgtttcc
     3721 ccctggtagc tccctcgtgc gctctcctgt tcctgccttt cggtttaccg gtgtcattcc
     3781 gctgttatgg ccgcgtttgt ctcattccac gcctgacact cagttccggg taggcagttc
     3841 gctccaagct ggactgtatg cacgaacccc ccgttcagtc cgactgctgc gccttgtccg
     3901 gtaactatcg tcttgagtcc aacccggaaa gacatgcaaa agcgccactg gcagcagcca
     3961 ctggtaatcg gattcacgga gcggagtaga gttatctaca gagttcttga agtggtggcc
     4021 tgactacggc tacactgaaa ggacagtttt ggtatctgcg ctccgtgaaa gccagttacc
     4081 ttcggaagaa agagttggta gctctaaatt ccggcaaacg aaccaccgtt ggtagcggtg
     4141 gtttttttgt ttacggctta ggagattacg gctagaacga aaggatctca agaagatcct
     4201 ctcagaaatt atacagacat gcggtagttt gagatgtcag agctatctaa ctcttttgcc
     4261 ggaacca
//
