LOCUS       NZ_CP100674             5177 bp    DNA     circular CON 23-JUL-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Mbandaka strain R17.0904
            plasmid pR17.0904_5.2k, complete sequence.
ACCESSION   NZ_CP100674
VERSION     NZ_CP100674.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN29431219
            Assembly: GCF_024266165.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Mbandaka
  ORGANISM  Salmonella enterica subsp. enterica serovar Mbandaka
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 5177)
  AUTHORS   Chiou,cs., Chen,bh., Wang,yw. and Teng,R.H.
  TITLE     28 Salmonella enterica strains that have azithromycin resistance
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5177)
  AUTHORS   Chiou,cs., Chen,bh., Wang,yw. and Teng,R.H.
  TITLE     Direct Submission
  JOURNAL   Submitted (30-JUN-2022) Center for Diagnostics and Vaccine
            Development, Centers for Disease Control, Taiwan, No.20, Wenxin S.
            3rd Rd., Nantun Dist., Taichung City 408, Taiwan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: No
            Genome Coverage                   :: 196x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/23/2023 02:20:20
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,803
            CDSs (total)                      :: 4,684
            Genes (coding)                    :: 4,565
            CDSs (with protein)               :: 4,565
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 119
            CDSs (without protein)            :: 119
            Pseudo Genes (ambiguous residues) :: 0 of 119
            Pseudo Genes (frameshifted)       :: 43 of 119
            Pseudo Genes (incomplete)         :: 84 of 119
            Pseudo Genes (internal stop)      :: 24 of 119
            Pseudo Genes (multiple problems)  :: 30 of 119
            Pseudo Genes (short protein)      :: 1 of 119
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP100674.1.
            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..5177
                     /organism="Salmonella enterica subsp. enterica serovar
                     Mbandaka"
                     /mol_type="genomic DNA"
                     /strain="R17.0904"
                     /serovar="Mbandaka"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:192954"
                     /plasmid="pR17.0904_5.2k"
                     /geo_loc_name="Taiwan: Chiayi County"
                     /collection_date="2017"
                     /collected_by="Centers of Disease Control, Taiwan"
                     /subtype="ST413"
     gene            complement(377..793)
                     /locus_tag="NL713_RS23930"
                     /old_locus_tag="NL713_23930"
     CDS             complement(377..793)
                     /locus_tag="NL713_RS23930"
                     /old_locus_tag="NL713_23930"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001283459.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_032419562.1"
                     /translation="MSDQKNNLDIQKQTLESKWGKEALSMGWSAIPTSLFFLQGALNMT
                     PTTFNVLLHLIIHWWKPYDWPHPSQESIAVRMGVSSRTVQRSLQELENYGLLTKIRTSK
                     DNPKYKGRNIYDMSLLVKSLNILTPDLNAKLNEK"
                     /name="helix-turn-helix domain-containing protein"
     gene            1141..1815
                     /locus_tag="NL713_RS23935"
                     /old_locus_tag="NL713_23935"
     CDS             1141..1815
                     /locus_tag="NL713_RS23935"
                     /old_locus_tag="NL713_23935"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001259273.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NYN domain-containing protein"
                     /protein_id="WP_032419561.1"
                     /translation="MRTIVYVDGFNFYHGLVKRSGYKWLDLYKLFEEQLLPIRARESQL
                     IQVKFFTAEIKAKFASRGELAHQAQQAYHRALVQIYGDKLQIIKGYYSERQECAMTFNE
                     GHPPSKTDRTTVWKLEEKQTDVRMALEMYRDAIRGEVEQLVLCTNDSDMIPPIEMIKAD
                     RPELKIGIVVPREQDTSRVISNLASLGDWSLPYVSYEALRLALLPDKVPTRRKPILKPN
                     HW"
                     /name="NYN domain-containing protein"
     gene            2805..3125
                     /locus_tag="NL713_RS23940"
                     /old_locus_tag="NL713_23940"
     CDS             2805..3125
                     /locus_tag="NL713_RS23940"
                     /old_locus_tag="NL713_23940"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /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_042863636.1"
                     /translation="MLTMWVTEDEHRRLLERCDGRQLAAWMRQTCLDEKPARAGRLPSI
                     SPALLRQLAGMGNNLNQIARKVNAGGAGHDRVQIVAALMAIDAGLERLRHAVLEKGGDD
                     DR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3334..>3765
                     /locus_tag="NL713_RS23945"
                     /old_locus_tag="NL713_23945"
                     /pseudo=""
     CDS             3334..>3765
                     /locus_tag="NL713_RS23945"
                     /old_locus_tag="NL713_23945"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /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            3803..4288
                     /locus_tag="NL713_RS23950"
                     /old_locus_tag="NL713_23950"
     CDS             3803..4288
                     /locus_tag="NL713_RS23950"
                     /old_locus_tag="NL713_23950"
                     /inference="COORDINATES: protein motif:HMM:NF016710.2"
                     /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_000096578.1"
                     /translation="MSSLLALAKDLEQQSKAQQQSTGEMLKAAFSEHEKSVKAELSASA
                     KRISDAISAHEQGMTAAMQSNRLSVLRMVGRTWLTITLVSVLLIATSGSILWWQGQQIT
                     GNYQTIRAQERTQAMLSEKNHGVQLSLCGEKKLSCVKVNPKAGAYGEEGNWMVLERK"
                     /name="MbeB family mobilization protein"
     gene            4292..4504
                     /locus_tag="NL713_RS23955"
                     /old_locus_tag="NL713_23955"
     CDS             4292..4504
                     /locus_tag="NL713_RS23955"
                     /old_locus_tag="NL713_23955"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137423.1"
                     /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_054175659.1"
                     /translation="MTELEKQLLTALEQLHQDYSQRLDEWESAFAEWQKMSGLMQRENA
                     ALNERVTRLSQQVANLSGQLQRLSQ"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(4873..5136)
                     /locus_tag="NL713_RS23960"
                     /old_locus_tag="NL713_23960"
     CDS             complement(4873..5136)
                     /locus_tag="NL713_RS23960"
                     /old_locus_tag="NL713_23960"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010891192.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_054175658.1"
                     /translation="MAAYTSETEKFLQSVSSDQTWWKSRYNPGDSVPHSGIYRCTVCGK
                     EITSNGSDPFPPQNHHQHSQQQAIKWQLIVRTDTKGDRFGIK"
                     /name="hypothetical protein"
     Typing          2517..2697
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="88.525"
                     /coverage="83.0"
                     /evalue="4.47e-55"
     Typing          complement(2058..2567)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.164"
                     /coverage="98.0"
                     /evalue="0.0"
     Typing          3116..4620
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.223"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gccgcccgct ggggcggctt ttcgttgcca gtctaaatat caagcatatt gggttaacat
       61 ccaggttaca gcctttcctg cgtacggagg cattacatta ccttttgcta tcggggctgt
      121 agtggaaggg gttcctacga ctttccagac accactttca ggacactttt gtccggtaga
      181 agcagtcgta ccaattggtg ctttagacat gctaattcct ctttttgtgt tttgtccgta
      241 ttgctgtttg tgtagcgata ctgatgttta gtttagaaat tagctttcaa tagggagctg
      301 ttgtcatttt ctagaaatgt gatgctgaac accttttgta cagtgatgtg cgcgctttgg
      361 ctgtcggaat ttttggttac ttttcgttta gtttggcgtt gaggtctggc gtaagaatgt
      421 ttagtgactt aactaaaaga gacatatcgt aaatgtttcg ccctttgtac ttagggttgt
      481 ccttgcttgt acgaattttt gtaagcaatc cgtaattttc aagttcttgg agtgagcgtt
      541 gaactgttct tgatgaaact cccattctaa ccgcgatgct ctcttgagat ggatgtggcc
      601 aatcataggg tttccaccag tggataatta gatgaagtag cacattgaat gttgtggggg
      661 tcatattgag tgcgccctgc aggaagaaaa gggatgtagg aatggctgac catcccatgc
      721 ttaacgcttc cttcccccat ttagactcaa gtgtctgttt ttgaatgtct aaattatttt
      781 tttgatctga catataccaa cctgctaagc tgaagtcttc taagaagact tcagcttagc
      841 aggttggtaa attaattcat ataattagta cgacaccagt gcgcttataa tatcattata
      901 tttaactata cttaatctac actcacctct tggtagcgcg attaagttac gcagctccct
      961 tgaggctcta aacctccctt taggtgggca gcgattaagt tacgcgtctt ccttcaggag
     1021 cttgaaaccg ccctctcggt tagttttaac cctgaggtac tacaacttaa actgtttgct
     1081 aacgttagtt tttgttgtta aaaccgccct tagaggcggt ttttttatgc gcgaaataaa
     1141 atgagaacaa tagtttacgt agatgggttc aatttttatc acggattggt taagcgttcg
     1201 ggatataagt ggttagacct ttataagctc tttgaagaac aactgcttcc gataagagca
     1261 cgagaatcac agttgattca ggtgaagttc tttactgctg agatcaaggc aaagtttgct
     1321 tctcggggtg aattggcgca ccaagctcag caagcctacc atcgagcatt agtacagatc
     1381 tatggcgata agctacagat aataaaaggt tattactcag agcgtcagga atgtgcaatg
     1441 acctttaatg aggggcatcc tccatcaaaa acggatagaa caacggtctg gaagttagaa
     1501 gaaaagcaga cagacgttag aatggcttta gaaatgtatc gcgatgcgat tcgtggtgaa
     1561 gtagaacaat tggttctctg cactaacgac tcagatatga taccgccaat agaaatgata
     1621 aaagctgatc ggcctgagtt aaaaatagga atcgtagtgc caagggaaca ggatactagt
     1681 cgagtgatta gtaatctggc tagtttaggg gattggagct tgccatatgt atcctatgaa
     1741 gccttaagat tagctttatt gccagataaa gtccccacta ggaggaagcc aatactgaag
     1801 ccaaatcact ggtaaacagc cggatcttct tgtgatcctt ttactttcgt cgtaatctca
     1861 tgccctgcaa acaaaaaaac caccgctacc aacggtggtt cgtttgccgg aatcaagagc
     1921 taccaactct ttttcccgaa ggtaactggc tttcacggag cgcagatacc aaaactgtcc
     1981 ttccagtgta gccgcagtca ggccaccact tcaagaactc tgtagaagca ctctactact
     2041 ctgctccgtg aatcctgtta ccagtggctg ctgccagtgg cgtttttgcg tgtctttccg
     2101 gattggactc aagacgatag ttaccggaaa aggcgcagcg gtcggactga acggggggtt
     2161 cgtgcataca gtccagcttg gagcgaactg cctacccgga actgagtgtc aggcgtggaa
     2221 tgagataaac gcggccataa cagcggaatg acaccggtaa accgaaaggc aggaacagga
     2281 gagcgcacga gggagccacc agggggaaac gcctggtatc tttaagtcct gtcgggtttc
     2341 gccaccactg atttgagcgt cagatttcgt gatgcttgtc aggggggcgg agcctatgga
     2401 aaaacggcag tgccgcatcc ttttcccgcc ctgcttgtca tgtcatatgc ctttgctctt
     2461 atccgtgtgt gcgtaacgcc cgccgcagcc gaacggcagg agcggaagcg accgagtgag
     2521 cgaggaggcg tcatatcacc gtaacctcca ttttctcctg tacgccctgt agctgcattt
     2581 tccccctgtc acatgaagca ctttcataaa gtgttactcc gccgtaacat attgagccag
     2641 tatacactcc gctagcgcta cgtgactggt tcagggctgc gccccgaaac ccgctaaaag
     2701 ccactgacgc gcctgcggct tgtccaacac cgtgccgacc gggaaacatt tcccgcccgt
     2761 cccggtgttc tcaggaggct actctggcag acaaacgcaa caagatgctc acgatgtggg
     2821 tgacggaaga cgaacaccgg cggctgctcg agcggtgcga cggcaggcag ctggcggcgt
     2881 ggatgcgtca gacctgcctc gatgagaagc cggcgcgtgc cggcagactg ccgtcgatat
     2941 cgccggcgct gctgcgccag cttgccggta tggggaacaa cctgaaccag atcgcccgga
     3001 aagtgaatgc cggtggtgcc ggtcatgacc gggtgcagat tgtggccgcc ctgatggcaa
     3061 tcgacgcggg actggagcgg ctgcggcatg cggtgctgga aaaagggggg gatgatgatc
     3121 gttaaatttc acccccgggg gcgcggtggt ggtgccggtc cggtggatta cctgctggga
     3181 aaagaccggc agcgcgaggg ggcgaccgtg ctgcagggaa aaccggagga agtccgggag
     3241 cttatcgatg cctcgccgta tgcgaaaaag tacacctccg gtgtgctgtc gttcgcggag
     3301 gctgaactgc cgcccgggca gcgggagcag atcatggcca gctttgagcg ggttctgatg
     3361 cccgggctcg ataaagacca gtacagcatt ctgtgggtgg agcacaccga caaggggcgg
     3421 ctggagctga atttcctgat ccccaacact gaactgctga ccgggaaacg cctgcagccg
     3481 tactacgatc gcgccgaccg gccgcgcatc gatgcctggc agaccgtggt gaacggcaga
     3541 ctggggctgc atgatccaaa cgccccggag aatcggcggt tactggtcac gccgtccgca
     3601 ctgccggaaa cgaagctgga agccgctcag gcgattacac gggggttgct ggccttagcc
     3661 tcatccgggg agctaaaaac gcgcgaggac gtcacagggg cgctcacagc ggcaggtttt
     3721 gaggtggtcc gcaccacaaa aaacagtatc agcattgccg acccggacgg ggggcgaaac
     3781 atccgactga agggagccat ttatgagcag tcttttagcg ctggcgaagg acttggagca
     3841 gcaatcgaaa gcgcagcagc agagtaccgg cgagatgctg aaagccgcat tcagcgagca
     3901 cgagaagtct gtaaaagcgg aactgagcgc aagcgcgaag agaatcagcg acgccatcag
     3961 cgcccacgag cagggtatga ccgcggcgat gcagtcgaac cggctgagcg tgctgcgtat
     4021 ggtcggccgg acgtggctga ccatcaccct ggtctcggta ctgctgatcg ccacgagcgg
     4081 gagcattctg tggtggcagg ggcagcagat caccgggaat taccagacta tccgggcgca
     4141 ggagcggacg caggccatgc tgtcggagaa aaaccacggc gttcagctgt cgctctgcgg
     4201 ggagaagaaa ctgtcctgcg tcaaagtgaa cccgaaagcg ggagcttacg gggaggaagg
     4261 gaactggatg gtactggaga ggaaatagcc catgacggaa ctggaaaaac agttgctgac
     4321 cgcattagag cagctacatc aggactactc gcaaaggctg gacgagtggg agagcgcctt
     4381 cgcggaatgg cagaagatgt ctggtcttat gcaacgggag aacgcggcgc tgaacgagcg
     4441 cgtgacgcgc ttgagtcagc aggtggcgaa cttgagcggg cagttacagc gtttgagcca
     4501 gtagtgcggc ggcatgaaat gacggtggcc gccgaacggg catacgagca gcgacagcac
     4561 gaaaaagaac tggcggaagc ccgttcccgg cagcggagct atgacggtcc gtcgctgggc
     4621 tgaaatgcag gaaagcaggg gtttcatcgg gtgtttacgc tgaaaccgga cgtcattcat
     4681 ctggctgcat ggctatgcag ccgggtaaaa tttatctgtc gcgaacgggg tggtttgtcg
     4741 ggtggtttgt tgccggtttt acctgactgc cgccccgttc gcggcgaacc cgtccggggc
     4801 ggtgcgggca agggatgtta tggtaaatat cttcgagctt caggtacaaa aaaagccccg
     4861 gagggctctc aatcatttga ttccgaaacg gtcaccttta gtgtccgttc tgacaatcaa
     4921 ttgccatttg attgcttgtt gctgactgtg ctgatgatgg ttttgcggcg ggaacgggtc
     4981 gctgccgtta ctggtgatct cttttccgca gacggtacat cgataaattc cagaatgggg
     5041 aacgctgtct cctggattat atcgtgactt ccaccatgtt tgatcgctac tgacgctttg
     5101 taaaaacttc tctgtttcgc tggtatatgc agccatttag ctttcctttt ctgaatttat
     5161 agggcagaga tagaaaa
//
