LOCUS       NZ_CP065133             4593 bp    DNA     circular CON 03-SEP-2023
DEFINITION  Salmonella enterica subsp. enterica strain 178 plasmid p178-5k,
            complete sequence.
ACCESSION   NZ_CP065133
VERSION     NZ_CP065133.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16807075
            Assembly: GCF_031038275.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica
  ORGANISM  Salmonella enterica subsp. enterica
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 4593)
  AUTHORS   Huang,T.-W.
  TITLE     Whole-genome sequencing of ceftriaxone-resistant Salmonella enterica
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4593)
  AUTHORS   Huang,T.-W.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-NOV-2020) Department of Microbiology and Immunology,
            School of Medicine, College of Medicine, Taipei Medical University,
            No. 250, Wuxin Street, Taipei 11031, Taiwan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2019
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 130x
            Sequencing Technology             :: Illumina, Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/01/2023 16:38:38
            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)                     :: 5,121
            CDSs (total)                      :: 5,002
            Genes (coding)                    :: 4,839
            CDSs (with protein)               :: 4,839
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 163
            CDSs (without protein)            :: 163
            Pseudo Genes (ambiguous residues) :: 0 of 163
            Pseudo Genes (frameshifted)       :: 54 of 163
            Pseudo Genes (incomplete)         :: 119 of 163
            Pseudo Genes (internal stop)      :: 25 of 163
            Pseudo Genes (multiple problems)  :: 32 of 163
            Pseudo Genes (short protein)      :: 1 of 163
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP065133.1.
            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..4593
                     /organism="Salmonella enterica subsp. enterica"
                     /mol_type="genomic DNA"
                     /strain="178"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:59201"
                     /plasmid="p178-5k"
                     /geo_loc_name="Taiwan"
                     /collection_date="2010-08"
     gene            complement(join(4544..4593,1..100))
                     /locus_tag="I0P23_RS25575"
     CDS             complement(join(4544..4593,1..100))
                     /locus_tag="I0P23_RS25575"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001326446.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032194431.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPERHVKTPLAAAIGNRLEELVLK
                     LCAG"
                     /name="hypothetical protein"
     gene            complement(770..961)
                     /locus_tag="I0P23_RS25580"
                     /old_locus_tag="I0P23_25375"
     CDS             complement(770..961)
                     /locus_tag="I0P23_RS25580"
                     /old_locus_tag="I0P23_25375"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_000165986.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1024..1347
                     /locus_tag="I0P23_RS25585"
                     /old_locus_tag="I0P23_25380"
     CDS             1024..1347
                     /locus_tag="I0P23_RS25585"
                     /old_locus_tag="I0P23_25380"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_001677263.1"
                     /translation="MLTIRVSDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGHWSSIDRVHVVAALMAIEGELRQLRQAVREQGGR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1556..>1990
                     /locus_tag="I0P23_RS25590"
                     /pseudo=""
     CDS             1556..>1990
                     /locus_tag="I0P23_RS25590"
                     /inference="COORDINATES: protein motif:HMM:NF015397.3"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            2025..2585
                     /locus_tag="I0P23_RS25595"
                     /old_locus_tag="I0P23_25390"
     CDS             2025..2585
                     /locus_tag="I0P23_RS25595"
                     /old_locus_tag="I0P23_25390"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_000067488.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKQQLDTLSTTVSTQLSTTEAELSRQQKNLLWQVIKGRVLFPALTA
                     LSVTGGIFLGCWGLIQWQESRIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            2592..2825
                     /locus_tag="I0P23_RS25600"
                     /old_locus_tag="I0P23_25395"
     CDS             2592..2825
                     /locus_tag="I0P23_RS25600"
                     /old_locus_tag="I0P23_25395"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137388.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHAVTQQNNA
                     ILNERVVNLSQQVQLLAGQVDRLSRLFITNNR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(3513..4352)
                     /locus_tag="I0P23_RS25605"
                     /old_locus_tag="I0P23_25400"
     CDS             complement(3513..4352)
                     /locus_tag="I0P23_RS25605"
                     /old_locus_tag="I0P23_25400"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354646.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001354646.1"
                     /translation="MLTLFIFFVLLIAACFFCFAPPRRGYDRNEIIPYKIKLSINKYRL
                     YIYSSGKVRQYLLFLVILSLYYSIAEPFKSELIKNISYSLMAAFIFDTGLNFSKENITK
                     GVISTRWHNDLYSSFERMKAINKIYYPSNKEINTEGLSKAITSSLFNDDANSFAKRDFR
                     LMWDLSSEKYLSYKEIIIRKGDKLDAVCLRFINDDYKFLVNFNRDEEVFKYFPSIMQPS
                     LKTYRALSRLVNSIKDPSRFKFTTESLEMELLEYLELRNELFNDIEEVMGSYAQRAP"
                     /name="hypothetical protein"
     Typing          598..682
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.03e-37"
     Typing          complement(29..587)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.583"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1338..2923
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ctgctgccag tggcgttttt acgtgtcttt ccgggttgga ctcaagacga tagttaccgg
       61 ataaggcgca gcggtcgggc tgaacggggg gttcgtgcac acagcccagc ttggagcgaa
      121 cgacctacac cgggccgaga taccaacagc gtgagctatg agaaagcgcc acgcttcccg
      181 aagggagaaa ggcggacagg tatccggtaa gcggcagggt cggaacagga gagcgcacga
      241 gggagcttcc agggggaaac gcctggtatc tttatagtcc tgtcgggttt cgccacctct
      301 gacttgagca tctgtttttg tgatgctcgt caggggggcg gagcctatgg aaaaacgcca
      361 gcggcgcagc cttcttcctg ttcctggcct tttgctcaca tgtttctttt ggcgttatcc
      421 cctgattctg tggataaccg catcaccgtc tttgagtgag ctgataccgc tcgccgcagc
      481 cgaacgaccg agcgtagcga gtcagtgagc gaggaagcgg aagagcgcct gatgcggcat
      541 tttctcctta cgcatctgtg cggtatttca caccgcatat ggtgcacttt tcttataatc
      601 cgcactgatg ccacatagtt aagccagtat acactccgct atcgctacgt gactgggtca
      661 gggctgcgcc ccgacacccg ctaaaacccg ctgacgcgcc ctgacgggct tgtctgctcc
      721 cggcatccgc tcacaggcaa gctgtgaacg tctccgggag ctgcatgttt cagttgcttt
      781 caccgtcatc gccgaagcgt gcgaggcaac tacggtagag ttcgtcggcg tggtcgtgaa
      841 gtgattcgca gatgtctgcc tgttcgtccg cgtccagctc gttgagtttt tccagcaggg
      901 tcagcgtctg gcttctgata aagcgggcca tgttaagggc tgttttttcc tgtttggtca
      961 tggtcttaag gctccttaat aggggatttt ttagggggaa tgataccgat gaaacgcgag
     1021 aagatgctca cgatacgggt tagcgatgag gagcacgccc ggttactgga acgctgcgag
     1081 ggtaaacgac tggcagaatg gatgcggcgg gtctgtctgg gggagccggt tgcgcgcaca
     1141 ggaaaactgc cgacactatc gccgccattg ctgcggcatc tggctgccat cgggaacaat
     1201 ctgaaccaga cagcccggaa ggtgaacagc ggccactggt cttcgattga ccgggttcat
     1261 gtggtggccg ctctgatggc catcgagggt gaattgcgcc agttgcggca ggctgtcagg
     1321 gaacaggggg gacgggatga tagttaaatt tcatgccagg gggaaaggcg gtggaagtgg
     1381 cccggtcgat tacctgctgg ggcgggagcg taaccgcgaa ggcgcaacgg tgctccgggg
     1441 taacccggaa gaaatccggg aactcattga tgccacgcca ttttcgaaga aatacacgtc
     1501 aggcgttctg tcgttcgcgg agaaggagtt accgccgggt gaacgcgaaa gagtgatgac
     1561 gagctttgag cgtgttctta tgcccggtct cgaaaaagac cagtacagca ttctctgggt
     1621 ggaacaccag gataaggggc ggctcgaact gaattttgtc attccgaaca tggaactaca
     1681 gagcggtaag cgcctccagc cgtactacga ccgtgcggac aggccgagga taaatgcctg
     1741 gcagacgctg gttaatcatc attacgggct gcgtgacccg aacgcaccgg agaacagacg
     1801 gacgcttgtc acaccgaata atctgccaaa agcgaaacag gaggccgcag aagcgattac
     1861 acggggtctt gaggcgcttt accgtgccgg agcaataaaa acgcgtcagg atgtcactga
     1921 ggcgctcaca gcggcaggtt ttgaggtggt gaggacaacc agaagcagta tcagtattgc
     1981 cgacccggag ggggggcgga atctcaggct aaagggggcg ctgtatgagc aatcttttac
     2041 aaatgggaac ggacttcgag aagaaactga aagagcgagc cgcttctacc gagaacatgc
     2101 tgaacagcga gttcaggaag ctagaagagt ctgtagacaa ggcactgagc ttaaacaggc
     2161 agaaaatcag agacgctatc agcgaacata caacatccgt gaaacagcaa ctggatacgc
     2221 tgagcaccac cgtgagcacg cagctcagca ccacagaggc cgaactgtcc cggcagcaga
     2281 aaaacctgct ctggcaggtg atcaaagggc gggtactgtt tccggcgctg accgcgctca
     2341 gcgtcacggg cggcattttc ctggggtgct gggggctgat tcagtggcag gaaagcagga
     2401 ttgcgaaaaa tatcttgacc atcagagagc aggaaaacac gctggcgaaa ctcgaggcaa
     2461 aaacctgggg ggtgacgttc gtcaatggcg agaacgggaa atttctggtg ctgccggacg
     2521 gggtgaaagg ggaaaacacc tggacggtgg gcgacaagaa cgccgtgagg ctggtcaggg
     2581 agtaaacgag tatgacggaa ctggaagggc atttgctgaa cgccttagag catttgcaac
     2641 aggactatat gcggcggctg aacgagtggg agagcgcctt cgcagaattg cagaagatgc
     2701 acgcggttac gcaacagaac aacgcgatac tgaacgagcg tgtcgtgaac ttgagtcagc
     2761 aggtgcagct attagccgga caagtcgacc gcttgagtcg gttatttatc acgaacaaca
     2821 gataagggat gaacaggagc gtcaggcgca ggagcttgcc cggcgctggc atgaagagca
     2881 ggaacccgaa gcgcggatct ggcgtggccc gtcaatgggg atgtgaccgg ggtaccccct
     2941 gaaatcgagc cagtttgtgg cacgccctac ccggatggcg ccaatgttaa tgtacgtaca
     3001 ttagcattaa caatatccaa acctccccat tttgccccgt tcgacggctg gaacgtgcga
     3061 aactgatcgt cattcagttt cgcgcataac tatgcatgag gttaaaattt accaggcgcg
     3121 atcgcggcag tttttcgggt ggtttgttgc tgtttttacc tgtctgctgc cgtgatcgcg
     3181 ctgaacgcgt ttaagcggta cgcgcaatgc gacgttatgg taaatacgga gtattttaat
     3241 tgcgggcctt tgttgtatat ctctgtcgtt tgtccccggg gggaagcatt actgctaaca
     3301 agtcccgtga gaaaactgcg caatcgtatt gcgcaccatg aacctattct caaccgcaat
     3361 ctggaggatg attttgctac gataaagaga attatcgcgt atcggtgtca gcattcattg
     3421 gagtggatgc tgaaaaacca ggtgttactc cctctactta cacttaaacc tctctaaaaa
     3481 tataagtaag tactatcgag ggctatcatg aactatggtg ccctctgagc atagctaccc
     3541 attacttctt ctatgtcatt gaataattca tttcttaact ctaagtattc tagtaactcc
     3601 atttctaatg actctgtcgt gaacttaaat ctagaaggat ctttgattga gtttactagt
     3661 cttgataacg ctctatatgt tttgagtgaa ggttgcatta tagatggaaa gtatttgaaa
     3721 acctcttcat ctctgttgaa attaactaaa aacttgtagt catcatttat aaatctcaag
     3781 catacagcgt caagcttatc gccttttctt attattattt ctttatagga aagatatttt
     3841 tcagaagata agtcccacat caagcgaaaa tctctctttg cgaacgagtt cgcgtcatca
     3901 ttgaaaagag atgatgtgat ggctttggat agaccttctg tgtttatctc tttgttggat
     3961 gggtagtaaa ttttattaat tgctttcatt ctctcaaatg atgaatatag gtcattatgc
     4021 caccttgttg aaatcactcc tttagttata ttctccttgc taaaattaag ccctgtatca
     4081 aaaataaatg cagccatcag tgaatatgat atgtttttta ttaactcaga cttaaatggt
     4141 tccgctatgg agtagtacag tgataaaata actaaaaata aaaggtattg tcttaccttt
     4201 cccgatgagt atatgtaaag gcgatattta tttattgata gttttatttt gtatggaatg
     4261 atctcatttc tgtcatatcc tcttcgtggt ggagcaaaac aaaagaaaca tgcagctatt
     4321 aataaaacaa aaaagatgaa cagtgtaagc aagttcggct cctgtgtatg ctcactatgc
     4381 atgattgtct tgagatctaa cgatcctgaa ggtagtcttg tccgtaaacg aaaaaaccgc
     4441 ccagcaaggc ggcttttcga aggttctcag agcagcaact ctttgaacca aggtaactgg
     4501 cttggaggag cacagccacc aaatctgtcc tttcagttta gccttaaccg gcgcataact
     4561 tcaagactaa ctcctctaaa cggttaccaa tgg
//
