LOCUS       NZ_CP065570             5570 bp    DNA     circular CON 31-MAY-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain
            R18.1078 plasmid pR18.1078_p5.5k, complete sequence.
ACCESSION   NZ_CP065570
VERSION     NZ_CP065570.1
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 5570)
  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  JOURNAL   Unpublished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 5570)
  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
            CP065570.1.
            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..5570
                     /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_p5.5k"
                     /geo_loc_name="Taiwan"
                     /collection_date="2018"
                     /collected_by="Linkou Chang Gung Memorial Hospital"
                     /subtype="ST34"
     gene            complement(join(5394..5570,1..342))
                     /locus_tag="I7656_RS26450"
     CDS             complement(join(5394..5570,1..342))
                     /locus_tag="I7656_RS26450"
                     /function="essential for mobilization of the plasmid"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001447511.1"
                     /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_031942530.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNNEFRRLGESVSEAVTSNE
                     TKIRDAIALFTASTEKSLEKHREGVKEAMMQHRKDVLKLAGNTGMMLLGIVFLLFTASG
                     GTLWYLGGRIQANLEEIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVIPFQ
                     GKEWVHLKE"
                     /name="MbeB family mobilization protein"
     gene            complement(<380..1078)
                     /locus_tag="I7656_RS26455"
                     /pseudo=""
     CDS             complement(<380..1078)
                     /locus_tag="I7656_RS26455"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /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            complement(1020..1343)
                     /locus_tag="I7656_RS26260"
                     /old_locus_tag="I7656_25570"
     CDS             complement(1020..1343)
                     /locus_tag="I7656_RS26260"
                     /old_locus_tag="I7656_25570"
                     /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_000956000.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGTR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1408..1599
                     /locus_tag="I7656_RS26265"
                     /old_locus_tag="I7656_25575"
     CDS             1408..1599
                     /locus_tag="I7656_RS26265"
                     /old_locus_tag="I7656_25575"
                     /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_137420181.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDDENH"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2269..2430
                     /locus_tag="I7656_RS26460"
     CDS             2269..2430
                     /locus_tag="I7656_RS26460"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354639.1"
                     /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_071596883.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHALTPLAAATGNRISRARFI
                     QMLTEFLK"
                     /name="replication initiation protein"
     gene            complement(2622..3578)
                     /locus_tag="I7656_RS26270"
                     /old_locus_tag="I7656_25580"
     CDS             complement(2622..3578)
                     /locus_tag="I7656_RS26270"
                     /old_locus_tag="I7656_25580"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014640333.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0009036 - type II site-specific deoxyribonuclease
                     activity [Evidence IEA]"
                     /GO_process="GO:0009307 - DNA restriction-modification
                     system [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II restriction endonuclease"
                     /protein_id="WP_232251742.1"
                     /translation="MKKLSSRYKRLFFMQRLSPGEFKTLISKERKSHFITPFALVYKTF
                     CDLGYDQKNSDYFLNNPSEYIIAMRKNCWKEFEPFEKEFTTRMLSYLIDEERIKDMSPY
                     DAIRDFTMEYPTHIYDLALSNTQSRRSRAGKEFESILELLMMGAGIPVDVQGAIGKSFF
                     QKNQIGKLVDLVMPGVVQYTSNKRNTMLISAKTTLRERWQEVPEEVNRTGIREMYLATL
                     DDSFSEETINILYEANVVVVTTVENKNFKYKNNNRVLTFEDMLQSAMELSRKWNNVSYT
                     DSEKEEIQQSILKQIEKYSDLPYVVNYYRNRLSALFD"
                     /name="type II restriction endonuclease"
     gene            3649..4788
                     /gene="dcm"
                     /locus_tag="I7656_RS26275"
                     /old_locus_tag="I7656_25585"
     CDS             3649..4788
                     /gene="dcm"
                     /locus_tag="I7656_RS26275"
                     /old_locus_tag="I7656_25585"
                     /EC_number="2.1.1.37"
                     /function="DNA methylation"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000131511.1"
                     /GO_function="GO:0003886 - DNA
                     (cytosine-5-)-methyltransferase activity [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-5-)-methyltransferase"
                     /protein_id="WP_031942531.1"
                     /translation="MTDNIAATIKEKRERLHMTQKEFADALGLSKYGDRTIRRWERGET
                     KPTGAELKAVMDFPDTPPYPNNENGRYRMIDLFAGIGGTRLGFHQTNAVNVVFSSEWDK
                     FAQKTYHANYGDFPDGDITKIDEKDIPDHEILVGGFPCVAFSQAGLKKGFNDTRGTLFF
                     DIARIIKEKKPHAFLLENVKNLLGHDKGRTFSIIKNTLEELNYTVYYNIFAAKDFGVPQ
                     NRERIYIVGFNKEKVRNHEHFTFPTPLKTKTRVGDILEKSVDNKYTLSDALWNGHQRRK
                     LVNAAAGKGFGYGLFNENSPYTNTISARYYKDGSEILIEQKGSNPRKITPREASRLQGF
                     PSDFIIPVSDTQAYKQFGNSVAVPVINAIAEKIISTLDS"
                     /name="dcm"
     gene            complement(5154..5387)
                     /locus_tag="I7656_RS26280"
                     /old_locus_tag="I7656_25590"
     CDS             complement(5154..5387)
                     /locus_tag="I7656_RS26280"
                     /old_locus_tag="I7656_25590"
                     /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_004026237.1"
                     /translation="MTELEIHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          complement(1688..1772)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.674"
                     /coverage="100.0"
                     /evalue="6.569999999999999e-34"
     Typing          1795..2341
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.182"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(3..1030)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.668"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(5051..5568)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.556"
                     /coverage="99.0"
                     /evalue="1.9e-76"
ORIGIN
        1 tatcctcccg ccaagatacc agagcgtccc gccactcgcg gtaaacagga gaaagactat
       61 ccccagtaac atcatgcccg tattccctgc cagctttaac acatccttcc tgtgctgcat
      121 catcgcctct ttcacccctt cccggtgttt ttccagcgat ttctctgtcg aggctgtgaa
      181 cagggctata gcgtctctga ttttcgtctc gtttgatgtc acagcctcgc ttacagattc
      241 gccgagcctc ctgaactcgt tgttcagcat tttctctgta gattcggctc tctctttcag
      301 ctttttctcg aactccgcgc ccgtctgtaa aagattgctc ataaaatgct cctttcagcc
      361 tgatattcct cccgccgttc gggtctgcaa tgctgatact gcttcgcgtc accctgacca
      421 cttcaatccc tgcctccgtg agcgcctgaa tcacatcctg acggcctttt atctccccga
      481 catgataaag agcgtctatc ccgcgtgtga cgctctctgc aagcgcctgt ttcgtttccg
      541 gcaggttatc agggagagtc agtatccggc ggttctccgg ggcgttgggg tcatgcagcc
      601 cgtaatggtg attaaccagc gtctgccagg catcaattct cggcctgtct gcccggtcgt
      661 agtacggctg gaggcgtttt ccgctctgta gctccatgtt cggaatgaca aaattcagct
      721 caagccgtcc cttgtcctgg tgctccaccc acaggatgct gtactgattt ttttcgagac
      781 cgggcatcag tacacgctca aagctcgcca tcactttttc acgtcctccc ggcggcagct
      841 ccttctccgc gaacgacaga acacctgacg tgtatttctt cgcaaatggc gtggcatcga
      901 tgagttcccg gacttcttcc ggattaccct gaagcaccgt tgccccttcc cggttacgct
      961 cccttcccag caggtaatca accggaccac tgccaccacc ttttcccctg gcatgaaatt
     1021 taactatcat cccgcgtccc ctgttccctg acggccagac gcagccggcg cagctcatcc
     1081 ccgatggcca tcagtgcggc cactacctga acccggtcac cggaagacca ctgtccgctg
     1141 ttcaccttcc tcgctgtctg attcaggtta ttcccgatag cggccagctg acgcagtaac
     1201 ggcggtgcca gtgtcggcag tttcccggaa cgggcaaccg gctcacccag gcagacccgc
     1261 cgcatccata ctgccagttg tttaccctca cagcgttcaa gtaacctggc atgttcatca
     1321 tcagtaaccc gtatcgtgag catcctctcg cgtttcatcg gtatcattac cccatgaaca
     1381 gaaatacccc cttacacgga ggcatcagtg actaaacagg aaaaaaccgc ccttaacatg
     1441 gcccgcttta tcagaagcca gacattaacg ctgctggaga agctcaacga actggacgca
     1501 gatgaacagg cagacatctg tgaatcgctt cacgaccacg ccgatgagct ttaccgcagc
     1561 tgcctcgcac gtttcgggga tgacgatgaa aaccactgac acatgcagct cccggagacg
     1621 gtcacagctt gtctgtgagc ggatgctggg agcagacaag cccgtcaggg cgcgtcagca
     1681 ggttttagcg ggtgtcgggg cgcagccatg acccagtcac gtagcgatag cggagtgtat
     1741 actggcttaa ctatgcggca tcgatgcgga ttgtatgaaa agtgcgccat ggacggtgtg
     1801 aaatgccgca cagatgcgta aggagaaaat gcaacttccg acactcttcc gcttcctcgc
     1861 tcactgactc gctacgctcg gtcgttcggc tgcggcaagc ggtgtcggct cactcaaagg
     1921 cggaaatacg gttatccaca gaatcagggg ataaggccgg aaagaacatg tgagtaaaaa
     1981 ggcaaagtgc aacaaaaggc cgcgccgctg gcgtttttcc ataggctccg cccccctgac
     2041 gagcatcaca aaaatcgacg ctcaagtcag aggtggcgaa acccgacagg actataaaga
     2101 taccaggcgt ttccccccgg aagctccctc gtgcgctctc ctgttccgac cctgccgctt
     2161 accggatacc tgtccgcctt tctcccttcg ggaagcgtgg cgctttctca tagctcacgc
     2221 tgttggtatc tcggcttggt gtaggtcgtt cgctccaagc tgggctgtgt gcacgaaccc
     2281 cccgttcagc ccgaccgctg cgccttatcc ggtaactatc gtcttgagtc caacccggta
     2341 agacacgcct taacgccact ggcagcagcc actggtaacc ggattagcag agcaagattt
     2401 atccagatgc ttacagagtt cttgaagtga tggcctaact acggctacac tggaaggaca
     2461 gtatttggta tctgtgctct gctgaagcca gattacctcg gttagataat ctgccaggat
     2521 tagctaacct tcgaaaaaac cacctgccag ggtggttttt tcgtttacag gtccaagatt
     2581 acgcgcagaa aaaaaagatc tcaagagatc cttttagttt tttagtcaaa aagagcacta
     2641 agcctatttc tataataatt aacaacataa ggtaaatcac tatatttttc tatttgtttt
     2701 aatattgact gttgaatttc ctctttttca gagtctgtgt aacttacatt attccacttt
     2761 cttgataatt ccattgctga ctgtagcata tcttcaaagg ttagcaccct attattattt
     2821 ttatatttga aatttttatt ttctaccgtc gttacaacga ccacattagc ctcgtacaat
     2881 atatttattg tctcctcgct aaaagaatca tctagtgtag ctagatacat ttctctaatt
     2941 cctgttctat taacctcttc aggtacttct tgccatcgct ccctcagcgt tgttttagcg
     3001 gaaatcaaca ttgtatttct tttgttagat gtgtactgga ctacacctgg cataacaaga
     3061 tctacaagtt tacctatttg gtttttttga aaaaatgact tcccaatagc cccctgcaca
     3121 tcaacaggaa ttcctgcccc catcattaat agctcaagaa tagactcaaa ctcttttcct
     3181 gccctgctac gtctggattg agtgttagac agtgccaaat catatatgtg tgtagggtat
     3241 tccatcgtaa aatcacgaat ggcatcataa ggactcatat cttttattct ttcttcatca
     3301 ataagatatg ataacattct tgttgtgaat tctttttcaa atggttcaaa ttctttccaa
     3361 cagttttttc tcattgcaat tatatattca cttggattat tcaaaaaata atcactattt
     3421 ttttgatcat accctaaatc acaaaatgtt ttataaacca aagcaaatgg cgtaataaaa
     3481 tgcgactttc tctctttaga aattagagtt ttaaattcac caggacttaa tctttgcata
     3541 aaaaataacc ttttatatct acttgaaagt tttttcatgc acgttcataa ttggaatcaa
     3601 aacaggacaa attgtcctaa aaccaacact taattctggt agacatgcat gactgataat
     3661 atcgcagcaa caatcaaaga aaaaagagaa agacttcata tgactcaaaa agagtttgca
     3721 gacgcccttg gtctttcaaa atatggagac agaaccataa gaagatggga gcgcggggaa
     3781 acaaaaccta ctggggcgga actaaaagca gttatggact ttccagacac accaccttac
     3841 ccaaacaacg agaatggcag atatcgcatg atcgatttat ttgctggaat cggtggaacc
     3901 agacttggat ttcatcaaac taacgctgta aatgttgttt tttccagcga atgggataag
     3961 tttgctcaaa agacatatca tgcaaattat ggtgatttcc ctgatgggga cataacaaaa
     4021 atcgatgaaa aagatattcc tgatcatgaa attcttgtcg gtgggtttcc ttgcgtagca
     4081 ttctctcaag cagggctcaa aaaaggattt aatgatacaa gaggaacttt gttttttgat
     4141 atagcaagga taataaagga aaaaaaacct catgcttttt tacttgaaaa tgtaaaaaac
     4201 ttgctagggc atgataaagg tagaactttt tcaataataa aaaatacact tgaagaattg
     4261 aattacactg tgtattacaa tatcttcgct gcaaaagact ttggtgttcc acaaaataga
     4321 gaacgcatat acattgtagg ctttaataaa gaaaaagtaa gaaatcatga acattttact
     4381 tttccaaccc cattaaaaac aaaaacaaga gttggagata ttcttgaaaa gagcgtagac
     4441 aataaatata cgctatcaga tgcgctctgg aatggacacc aacgcaggaa acttgtaaat
     4501 gcagcagccg gtaaaggctt tgggtatggt ttatttaatg aaaatagccc atatactaat
     4561 accataagtg cgaggtacta taaagatggt agcgaaatat taatagagca aaaaggaagt
     4621 aacccaagaa aaataactcc gcgggaagcg tcaagacttc aagggtttcc tagtgatttt
     4681 attatccctg tatcggatac acaggcttat aagcaatttg ggaattcagt cgcagtccct
     4741 gttatcaatg caatagcaga aaaaatcata tcgaccttag attcataaac taagtcataa
     4801 ggacacaatg cggctcagaa tccaattccc cccccatatg gatttaccat aacgtcgcat
     4861 tacgcgcacc gctaaaacgc gttcagcacg atcacggcag cagacaggta aaaatggcaa
     4921 caaaccaccc gaaaaactgc cgcgatcgcg cctgataaat tttaaccgca tgaataccta
     4981 tgcaaccaga tggcacaggc cacattaacc cctcttaatc cactgaagct gccatttttc
     5041 atggtttcac catcccagcg aaggaccatc cagcgtgcgt tcctgtattt ccggctgacg
     5101 ctcccgttcc agggataatg catgttcgcg ctcctgtatc agccgttcct ctcttatctc
     5161 cagttctcgc tgtataactg gctcaagcgt tctgtctgct cgctcaagtg ctgcacctgc
     5221 tgactcaact gcatgacccg ctcgttcagc atcgcgttgt cccgttgcgt aagcgaaaac
     5281 atcttctgca attccacgaa ggcgctctcc cattcgctca gccgctgcat atagtcctgt
     5341 tgcagctgct ctaaggcgtt cagcaaatgt atttccagct ctgtcactct gtgtcactcc
     5401 ttcagatgta cccactcttt cccctgaaag ggaatcacct ccgctgattt cccgtacgga
     5461 aggacaagga atttcctgtt cccgtcctgc acaaactcca cgccccatgt cttcgcgttc
     5521 agtttctgca atgtctcttc ctgcttcctg atttcttcca ggttcgcctg
//
