LOCUS       NZ_CP065571             4073 bp    DNA     circular CON 31-MAY-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain
            R18.1078 plasmid pR18.1078_p4k, complete sequence.
ACCESSION   NZ_CP065571
VERSION     NZ_CP065571.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16987173
            Assembly: GCF_016025415.2
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Typhimurium (Salmonella
            typhimurium)
  ORGANISM  Salmonella enterica subsp. enterica serovar Typhimurium
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 4073)
  AUTHORS   Chiou,C.-S., Hong,Y.-P., Wang,Y.-W. and Chen,Y.-S.
  TITLE     Salmonella enterica subsp. enterica serovar Typhimurium strain
            R18.1078
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4073)
  AUTHORS   Chiou,C.-S., Hong,Y.-P., Wang,Y.-W. and Chen,Y.-S.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-DEC-2020) 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 Date                     :: 30-MAR-2022
            Assembly Method :: unicycler v. 0.4.8; polca v. 4.0.5; polypolish v.
            0.5.0
            Genome Representation             :: Full
            Expected Final Version            :: No
            Genome Coverage                   :: 190.0x
            Sequencing Technology :: Oxford Nanopore MinION; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_016025415.2-RS_2024_05_31
            Annotation Date                   :: 05/31/2024 04:29:48
            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)                     :: 5,274
            CDSs (total)                      :: 5,151
            Genes (coding)                    :: 5,018
            CDSs (with protein)               :: 5,018
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 133
            CDSs (without protein)            :: 133
            Pseudo Genes (ambiguous residues) :: 0 of 133
            Pseudo Genes (frameshifted)       :: 38 of 133
            Pseudo Genes (incomplete)         :: 104 of 133
            Pseudo Genes (internal stop)      :: 23 of 133
            Pseudo Genes (multiple problems)  :: 28 of 133
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP065571.1.
            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..4073
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="R18.1078"
                     /serovar="Typhimurium"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pR18.1078_p4k"
                     /geo_loc_name="Taiwan"
                     /collection_date="2018"
                     /collected_by="Linkou Chang Gung Memorial Hospital"
                     /subtype="ST34"
     gene            complement(157..2304)
                     /gene="mobQ"
                     /locus_tag="I7656_RS26285"
                     /old_locus_tag="I7656_25595"
     CDS             complement(157..2304)
                     /gene="mobQ"
                     /locus_tag="I7656_RS26285"
                     /old_locus_tag="I7656_25595"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_001029354.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPHELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAIGPAGFSGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNGGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPKDSN
                     SAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQMAFEKQWQQWGESGLAALRAQL
                     LKREEELRRKEQEDTERSRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRTRIFESVDLMRDRSGYICDRSEIGQRPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSPAARKVDFMQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSLGGVIRLNGTLYPAFAVPSADNRHLVISALTDKGLRYA
                     GYGVAVNHDADSHISPAPELMQFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRTWEEW
                     QREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     gene            2483..2737
                     /gene="mobC"
                     /locus_tag="I7656_RS26290"
                     /old_locus_tag="I7656_25600"
     CDS             2483..2737
                     /gene="mobC"
                     /locus_tag="I7656_RS26290"
                     /old_locus_tag="I7656_25600"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091746.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     gene            3271..3972
                     /locus_tag="I7656_RS26295"
                     /old_locus_tag="I7656_25605"
     CDS             3271..3972
                     /locus_tag="I7656_RS26295"
                     /old_locus_tag="I7656_25605"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /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_001281395.1"
                     /translation="MSDLIAYKSNALIEASYKLTLQEQRFLLVCISRLKSGEDSPSPDE
                     QKTMTITAAEFHDAFPDMGRQHAEARLKEAIDRLWDRSVIIKNEEKREEFRWVQYRAQY
                     FKGEAKVDITFSDAIMPYLTQLKGQFTRVVVKNVSSLSSTYSIRIYELLQQFRSTGDRT
                     IAIDDFRTMLAVEDKYQQFKDLNKMIIKPAIAELNEKSDLVVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     Typing          complement(1947..2305)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2306..2482
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          3272..3972
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(161..2391)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.989"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tgcagcgaaa aaagaccccc caatttttgg gggcggaaaa acaaaactat gcttgcgtta
       61 tgtgagtgtg cttcttgcat tcatccctgt cgatgaacat cgaagaacat cgacgaacat
      121 aacacgatgt taaacaaaac aaaatattgt tcacattcac tgtgaccaac cgcgatcatg
      181 tctcctctcg gtggtgtgtg ttcgtgcatc ttcctcgcgc tgccattcct cccaggtacg
      241 attaaaaccc agcgagcgga acagatgatc cggctgtttt tctggtgtgt tgacggcagc
      301 aaaaagcggt gcctcacggg ttttcagatg aaactgcatc agttctggtg caggtgatat
      361 gtggctgtct gcatcgtgat ttacggcaac accataccct gcataccgta accccttatc
      421 ggtcagcgca ctgatgacca gatgcctgtt atcggctgag ggaacggcaa acgcgggata
      481 cagcgtacca ttaagccgga taacaccgcc cagagagtca tccacgccca tgaccagcaa
      541 aagctgaagc tggcgggttt cccggtcgac agaactcatg accggcatca gcgtcggtgg
      601 cagacgtccc tgcataaaat ccaccttcct tgccgctggt gatggcatgg ctggctggcg
      661 gtcttctcca agacagaaag actccggcca tgtcttcggc tggcggagat tgcgggtatg
      721 ttgcggccat gtctggcaaa cctgcgtcag cagttgctca aaggttgcag aggaataaac
      781 acgttgcagt ggcggacgtt ggccgatttc gcttcggtca cagatataac cactcctgtc
      841 acgcattaaa tcaacactct caaagattct ggtgcggtat ttctccagct cgttccccca
      901 gagcgtatat tctccgttcc ggttgtgaag cagaaggtaa caggtcattt ccccgttacc
      961 aggcatggga gcctcgccat accccgtaac gactgctctc agcacccctg aatccataac
     1021 ggcattgtca tttttcctga gctgctccgc gcgactacgt tcagtatctt cctgttcctt
     1081 ccggcgcaat tcctcttcac gtttaagcaa ctgggctctg agagctgcaa ggccggattc
     1141 cccccactgc tgccactgtt tttcaaatgc catctgactc gcgggaatgt cctgtttctc
     1201 caccttccgg taatgctgtc gtaatttttc catttgctgg ctcagagact ggatttttcc
     1261 ctgctcacta cggtattccg gtgccgccca ttgcatcagg ggaatacggg aaaaaccgga
     1321 cgaaaacggc gatgattttt tcaggctggc agcatggctc atcgcttcct ttcgttcggt
     1381 gttcagctct tcccagcgtc tgcgcgtcgc ctgcatatct gccatcatcg acatggcatt
     1441 actggtgagt ttccatgccg agttactgtc cttcggcaac gcttcgataa tgtcacgtag
     1501 tgtgtacgaa gttgcgttgt caggaagccc gatattcaga aggtcagcca cacggcgggc
     1561 aggctctgtc agccctccgt tcctgagttc ggtgcgggaa atctgtattt ccaggttaag
     1621 cctgttaatc agacgattct gttcgccgcg ttctgtttcg ataccgcgtg tttccatcgc
     1681 acaggcagac tttccgaggt gaataccagg cgttttctca agcccctgtc gctcgtatga
     1741 acgatggtct atctcttcct gataaccggc gttcgccagt gccctgtttg catggtcagc
     1801 ccatgatgcc cgccacgtct cggcatgtgt ccggtcgttc cagtccctga cctttccgct
     1861 gaacccagca ggtccgatag ccctcgtggt cagcatgatg tgcgcatggg gatttgtttt
     1921 atccatgtga tggaacgcca catcagcaat catgccctga ctgacaaagt tttctctgac
     1981 aaaggcgaga acggtttccc gtgcggcatc ctgcggcagt tcgtggggga tggcgagttc
     2041 aatttcccgc gcaagttgtg agttcttccg gcgttcggcc ttctcaacgg cattccagag
     2101 ttcggcacgg ttcgtacacc aggcaggggc ggtggcgggg gtcagaatca cagcctcagc
     2161 cacaccgctt ttgcgggtgt agtcgtgagt cagtccggta cgctcatcaa gcatcagtga
     2221 accggaacga taggcagcgg aagctacggc gctgtagccg ctgcttctgg agataatttt
     2281 catgctgaga tgataaatcg ccatttctgc cgtaatgcct ttttgtagtt ttctttcagc
     2341 cccgcagggc gcacacaatc gaaacggagt ggagattgta taagtgcgca cttcgtgatt
     2401 tgccgtgcat tatgccagct cagtttttaa actaccagtg acgcgctaaa atgcgatttt
     2461 tcatcgcgca cggagttaca tcatgagcag aacgctcgaa cagaagattg ctgatgctga
     2521 ggcgagatta cagcgcctga aggcgaagag ccggagcctg gacacagcgc agaaggttgt
     2581 tgtgggtgct gcattgctgg caaaggtcag aaagccggag gaggtgcagt tgcgtgcctg
     2641 gttactccag ttcctgaagg cagaggtgac acgacaggct gatgtgacgc gcatactgcc
     2701 gctgattaac gagctggagg cgctgccaga acagtgattg tatcgtccgc tcgccgcagc
     2761 cccagcgacc gagcgttagc gagcgagtgg gcgaggaagc ggaagtgaat cagtcgccag
     2821 gttgagcaca tacgcacggt ttttcggcag gtgatatgcg ctgaacccgc atgaatactg
     2881 ggtttccaca gggttggagg gggtgtattc gaaacttgca attctgcttt attgcaacgc
     2941 attgttttta ttggtttttt gttttcagca ccccaagtta tccacaggct cgccgttaag
     3001 tttttaagat cttattttta gatctttttt tttaaaacct ttttaggtct tgtaacacca
     3061 tgattttaaa gatgttctgg caagataagt ggagcttttg ggggtgaaag gtggagcttt
     3121 tgggggtgaa aggtggagct tttgggggtg aaaggtggag cttttggggg tgtaatccac
     3181 agaaaaaggg ggttacaaaa aaaaaacttc cacccatatg ataagtggcg tacagtaaaa
     3241 aaacgccacc aatagcaacg agcaagcgaa atgtcagatc tgatagctta caaatcaaac
     3301 gcccttatcg aggcaagcta caagctcact ttgcaggaac agcgcttcct gctggtctgt
     3361 atcagccgcc taaaatccgg agaagattcc ccttcgccgg atgaacaaaa aaccatgacc
     3421 atcacggctg cagagtttca tgatgccttt cctgacatgg gacggcagca cgctgaagct
     3481 aggctcaagg aagcgataga tcgcctctgg gacaggtcag taatcatcaa gaacgaggaa
     3541 aaacgagaag agttccgctg ggtgcagtac cgggcgcagt atttcaaagg tgaggcgaaa
     3601 gtagatatca ccttctccga tgccatcatg ccgtatctga cacagctcaa ggggcagttt
     3661 acgcgggtag tcgtgaagaa cgtctccagc ctttccagca cctacagcat ccgcatttac
     3721 gagctgctcc agcagttccg cagcaccggt gacagaacga tagctatcga tgatttccga
     3781 accatgcttg ccgttgaaga taaatatcaa caattcaaag acttgaataa gatgataatc
     3841 aagccagcca tcgccgaact gaacgaaaaa agcgatctgg ttgtaactgt tgagacgatc
     3901 aaaaaggggc gcacggttgt agccctgcat tttcgcttca aggaagacaa acagatcaag
     3961 atgacgatct aaaatcgatt ttaaggcacc taaaacgctc cctgctgcgt tttttttgtg
     4021 ttagtagtgc gaaggtacta ttgaagtgaa aaattgcgtc aaaaacgctc tga
//
