LOCUS       NZ_CP060836             4267 bp    DNA     circular CON 24-MAY-2024
DEFINITION  Salmonella enterica strain 1505 plasmid p1505-3, complete sequence.
ACCESSION   NZ_CP060836
VERSION     NZ_CP060836.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15941602
            Assembly: GCF_022559345.1
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  JOURNAL   Unpublished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_022559345.1-RS_2024_05_24
            Annotation Date                   :: 05/24/2024 04:13:58
            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)                     :: 4,760
            CDSs (total)                      :: 4,645
            Genes (coding)                    :: 4,516
            CDSs (with protein)               :: 4,516
            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)       :: 48 of 129
            Pseudo Genes (incomplete)         :: 93 of 129
            Pseudo Genes (internal stop)      :: 29 of 129
            Pseudo Genes (multiple problems)  :: 37 of 129
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP060836.1.
            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="1505"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:28901"
                     /plasmid="p1505-3"
                     /geo_loc_name="China: Hangzhou"
                     /collection_date="2015-08"
                     /collected_by="Meina Yue"
     gene            470..601
                     /locus_tag="IAR36_RS23875"
     CDS             470..601
                     /locus_tag="IAR36_RS23875"
                     /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            complement(821..1630)
                     /locus_tag="IAR36_RS23785"
                     /old_locus_tag="IAR36_23610"
     CDS             complement(821..1630)
                     /locus_tag="IAR36_RS23785"
                     /old_locus_tag="IAR36_23610"
                     /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(1623..2873)
                     /locus_tag="IAR36_RS23790"
                     /old_locus_tag="IAR36_23615"
     CDS             complement(1623..2873)
                     /locus_tag="IAR36_RS23790"
                     /old_locus_tag="IAR36_23615"
                     /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(3285..3653)
                     /locus_tag="IAR36_RS23795"
                     /old_locus_tag="IAR36_23620"
     CDS             complement(3285..3653)
                     /locus_tag="IAR36_RS23795"
                     /old_locus_tag="IAR36_23620"
                     /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(4024..4173)
                     /locus_tag="IAR36_RS23800"
                     /old_locus_tag="IAR36_23625"
     CDS             complement(4024..4173)
                     /locus_tag="IAR36_RS23800"
                     /old_locus_tag="IAR36_23625"
                     /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          63..579
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.192"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 tatgttacgg cgagatggag attcggggaa gtgcttcatg tggcaagggg gaaaatacgg
       61 ctgcggggcg taagtgcaaa atgcaggtaa cgatgaaatg acgcctcctc gctcactcgg
      121 tcgctgcgct cctgccgtga gactgcggcg ggcgttacca gctcacgaag gacgagataa
      181 cgagattgcg ctcaagtcag gaaagtcagg aaaaaggatg cggcgttgcc gtttttccat
      241 aggctccgcc cccctgacaa gcatcacaaa atctgacgct caaatcagtg gtggcgaaac
      301 ccgacaggac tataaagatc ccaggcgttt ccccctggta gctccctcgt gcgctctcct
      361 gttcctgcct ttcggtttac cggtgtcatt ccgctgttat ggccgcgttt gtctcattcc
      421 acgcctgaca ctcagttccg ggtaggcagt tcgctccaag ctggactgta tgcacgaacc
      481 ccccgttcag tccgactgct gcgccttgtc cggtaactat cgtcttgagt ccaacccgga
      541 aagacatgca aaagcgccac tggcagcagc cactggtaat cggattcacg gagcggagta
      601 gagttatcta cagagttctt gaagtggtgg cctgactacg gctacactga aaggacagtt
      661 ttggtatctg cgctccgtga aagccagtta ccttcggaag aaagagttgg tagctctaaa
      721 ttccggcaaa cgaaccaccg ttggtagcgg tggttttttt gtttacggct taggagatta
      781 cggctagaac gaaaggatct caagaagatc ctctcagaaa ttatacagac atgcggtagt
      841 ttgagatgtc agagctatct aactcttttg ccggaaccag tttgtaatgc ctttcctcaa
      901 tcaatttcac ttgtccttcg tctatcttta gctcaaacag tgcaatcaaa tcgctcgaaa
      961 caaactgagc ggaaatagct ctacatctaa catttgggta tttttgttca caccacgctg
     1021 tatcttgcga tgtttgcacc attgatattt gatctgtccc accttttgct tgaactggta
     1081 ttatataatg gcaaccgtat ttatctatac ctacataaag ttcatcgatc tctatttgac
     1141 caattccctt caccgtagtt cttaaatgat tctgtaaaga atatgtggtt atacctagaa
     1201 atatatctat tagccggtta tatctcacct tcgccagcaa tgcctgctcg tcgtctaaag
     1261 aataacctgt aattatctcc ggggtattgt ctggaatttt tattgccacc atattaggat
     1321 ttggcaaaat cctactaata gttactaatc taaatcgata ctttgaccta ccagccagct
     1381 caataatcca ctccttacct tctggctgag tcaacagaat actttctggc ataggcgttc
     1441 taaatctgat tgaatatata acatcaccaa cattagatgg gagttctata cctaaatctt
     1501 ttgcagcact gtttatctct aacctttcaa acaaaacctc taagtcacca tcaacatatt
     1561 tatcgaaaaa tatcttttct accaactgat ggtatctatt tttggacctt tcttttttat
     1621 ccttactcac aaacaacctc cttgttacta ttttttattc tcttagcaat tacatttgat
     1681 gacacaccaa acatagatgc agcatcggac atagaaatag caaccaaact ttcatcaccg
     1741 agtttgattt tcttcgttgg tttttttggc gtaacaccaa gaaccttcat aatctgcaag
     1801 ccaacacttc tagctagcat aggaggaaca ctattaccga cctgtctaaa tccatgccac
     1861 ttagtcacat gaaatctgaa ccaatcagga tatgaatgca gtcttgctgc ctctctgacc
     1921 gtgatgaccc taggatagat cggatgtata ggacgaggag atgtaaaagc acctctgtca
     1981 cttgctgttc ctgcccttaa agtattacat agcccattca tcgagagctt tttaaacctg
     2041 ctgattggtt ctaccgtgtc aggcaaagtt tcaacaaacc gccctctaga aatgtcagag
     2101 tgatctgtca gtaaagaaca cgttaatttg tctttattaa aaatccttgg gtagctaaaa
     2161 tcactaggat cttttcctac gccatgcaaa taggatgagt atagtgattg ctcaccaaat
     2221 ttagcataaa cccaatctct accccatagc tcaggatatt tttccgcatc aggaatatcc
     2281 ccaatagcgt ccccaaccgt tgttctaatg gataatggct cagggtatga tggcagagca
     2341 attcctttcc ttccccccat taagaaaaga cgacggcgat cttgaggaac tccataatca
     2401 gctgcgttta gcactttata atcgcttaca acgtcgtacc cgccatcttt aaatgcatcc
     2461 attatctcta ctaaaaactg cttatgctta ccaaccgtca acccttttac attttcaaaa
     2521 ataaagtatt taggctttag ctcaagaacc agccgtacat agtgatagac cagtttgttt
     2581 ctatcatcat caagcgcgcg ttttcctatt aatgaaaagc cttggcaggg agcgcctccg
     2641 atcactacat caatctcttt ctcaccaata cctgaaactt ccctaacgta ttctccggta
     2701 acatcaacaa cacttctaca tatcgttttg cacataggaa agttatattt gtgagcagag
     2761 caatgtattg gatctatttc aactgatgcc attatatcaa agccagcttg ctcgaaaccg
     2821 agactcagcc cacccgctcc agcaaataaa tcaacagcaa tcggtctagt cattctttac
     2881 acccacgtta tataaaatca acatgatgct atcagaaaaa cgatcgcttt accgatcgtt
     2941 tttctgattt cgattgaaca taacatccct tgcgtgcacc acctgagagg ccctcagggc
     3001 gtttctgacg ggaaaccggc aaaacaggca acaaaccacc cgaaaacccg ccagaaacgc
     3061 gcaggctctg tttttacggc atgcatgagt atgcgcgcaa gtgcatagcg cggaaattca
     3121 cgccattcag ccggggtaag tcctgtttcc ggcgttcttc ccatccgaaa acggtgaacg
     3181 ggcgggaaat ttattgcgtg gccgtgaggc gttggcaaga acatcaggca tgaagataag
     3241 ggggcggatg tacgaacgtt tcacaaaaca atttcgagtg gaaatcagaa ccccttcctc
     3301 ctgccaatgc tatccctcaa tgactcagcc agtctttgag attcatcttc cactcttctg
     3361 aagtcattca cggacagaaa aaaaccattc tctggcgcgc ctgctacaga aacagatttt
     3421 tctgtagcag gcaaagaatc cgctgtagcg agagacgatc catctgtatt ttttctcaac
     3481 ctgtaaagag ccttatcaaa cgcaacctgt gagatcttca gaccgtaacg ttcattcagt
     3541 acagccacaa tttctctcct ggggatgcca tttttcttcc agttttctat atcagccagg
     3601 gaatctctga cagccgcaat cgctgttctt ggaccaaggt taaaattcgc catacgccac
     3661 ccataatgtc ttatcaatgt ctcattttag tccaaaatat cacagaatgt cttataattg
     3721 tcctatcctt gtctttcacg gttcatgtag ccatgaaccg gcaggtatgt aacgcttttt
     3781 tatttcgctc aggcctgcca gatatagatt catgccttaa aagccaagtt gctttatccc
     3841 ttaaatggtc atacaccata cgcaatcgcg atttcatcgc aactgcatga atcaaatggg
     3901 aaaaatggga tttttcgttt atacgtgtaa tacgcaaggt attacagtca accgtaatta
     3961 catgaaaata aagaaataag atgtaatacc accgtattac acatacgctg gccagcgaaa
     4021 aagctataac gcttcccgac cgacaggagg cccggaatcc accggggcgt gcaggttatc
     4081 ttcagtaacc ttcgccatta aatcaaaaag gtcatactcg ccgggaagct gcgtatcagc
     4141 agcatcccgt tgttcatcat gttcagatgg catggggtga tatccagtag ctgagaggtt
     4201 gttagcgggt ttcggggcgc agccctgaac cagtcacgta gcgctagcgg agtgtatact
     4261 ggcttag
//
