LOCUS       NZ_AP023296             6835 bp    DNA     circular CON 23-SEP-2023
DEFINITION  Salmonella enterica subsp. enterica serovar 4,[5],12:i:- strain
            L-4261 plasmid pSAL4261-2, complete sequence.
ACCESSION   NZ_AP023296
VERSION     NZ_AP023296.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00097501
            Sequence Read Archive: DRR107045, DRR107046, DRR107047, DRR107048
            Assembly: GCF_019670245.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar 4,[5],12:i:-
  ORGANISM  Salmonella enterica subsp. enterica serovar 4,[5],12:i:-
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1
  AUTHORS   Sekizuka,T., Arai,N., Akiba,M. and Kuroda,M.
  TITLE     complete genome sequences of Salmonella enterica subsp. enterica
            serovar 4,[5],12:i:- str. L-4261
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6835)
  AUTHORS   Sekizuka,T., Arai,N., Akiba,M. and Kuroda,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (10-JUL-2020) Contact:Tsuyoshi Sekizuka National Institute
            of Infectious Diseases, Pathogen Genomics Center; 1-23-1 Toyama,
            Shinjuku-ku, Tokyo 162-8640, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: Canu v. 1.4; minimap v. 0.2-r124; racon v. 1.1.0;
            circlator v. 1.5.3; Pilon v. 1.18; SPAdes v. 3.11.1; A5-miseq v.
            20140604
            Genome Coverage                   :: 203x
            Sequencing Technology             :: Sequel; NextSeq500
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/23/2023 03:53:23
            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)                     :: 4,893
            CDSs (total)                      :: 4,771
            Genes (coding)                    :: 4,653
            CDSs (with protein)               :: 4,653
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 118
            CDSs (without protein)            :: 118
            Pseudo Genes (ambiguous residues) :: 0 of 118
            Pseudo Genes (frameshifted)       :: 38 of 118
            Pseudo Genes (incomplete)         :: 91 of 118
            Pseudo Genes (internal stop)      :: 19 of 118
            Pseudo Genes (multiple problems)  :: 28 of 118
            Pseudo Genes (short protein)      :: 1 of 118
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP023296.1.
            Annotated by DFAST v.1.0.8 (https://dfast.nig.ac.jp).
            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..6835
                     /organism="Salmonella enterica subsp. enterica serovar
                     4,[5],12:i:-"
                     /mol_type="genomic DNA"
                     /strain="L-4261"
                     /serovar="4,[5],12:i:-"
                     /isolation_source="Bos taurus"
                     /sub_species="enterica"
                     /db_xref="taxon:440524"
                     /plasmid="pSAL4261-2"
                     /geo_loc_name="Japan"
                     /collection_date="2014"
     gene            101..2083
                     /locus_tag="K5635_RS24255"
                     /old_locus_tag="SEL4261_P2010"
     CDS             101..2083
                     /locus_tag="K5635_RS24255"
                     /old_locus_tag="SEL4261_P2010"
                     /EC_number="2.1.1.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015966094.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0008168 - methyltransferase activity [Evidence IEA];
                     GO:1904047 - S-adenosyl-L-methionine binding [Evidence
                     IEA]"
                     /GO_process="GO:0006306 - DNA methylation [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="site-specific DNA-methyltransferase"
                     /protein_id="WP_031603854.1"
                     /translation="MQTELIKELNKVLKAFPQFWNGEELQRSMVSDAISQKQPDLIKAL
                     VDNEKVRSVYGADIDGIFIFDFDKLCGLLKYKEYWANSFTKYRNKVGLTSEGKYLDYSS
                     DVVLDFPFKDCVLEGGMSKEDQGKSEVYYNEIIARDEIDHLFSPKVLKEVNRYSKEGVK
                     KERIFNRNDNLIIRGNNLIALHCIKNIYEKSVKLIYIDPPYNTDTDSFKYNDKFSHSTW
                     LTFMKNRLEVAKDLLCDDGLIAISIDDNELNYLASLADDIFGRKNRIAIFPRITKKGGK
                     SASIFAKNHDYILLYVRSLENKRMYAVSHDDDNFKYKDEYFAERGSYKLNQTLDYDSLQ
                     YSKSLDYIIEINGEKYYPGGDENLFNDRMNGKHNRADWAWRWSRKLFDFGFENGFIEIR
                     NGGQRPRIYTKTYQNAKISKDGNDYVITYFDRTKPLSTLEFTENKYSNDNATKHISSLL
                     GKNIFDYTKPETLLAKLIEITSTKNDLILDFNLGSGTTAAVAHKMGRRYIGIEQMEYIN
                     DITVPRLKKVIEGEQGGISKDVNWQGGGSFVYAELMELNAYFVHEIQKAQSTEELEKLF
                     TMMKTEAHLNYQVELENVLSAEYEVDGIFRKVAFSELELHEQKQLLIEILDKNKLYVNV
                     SDMEDSELSISESDKAFTRSFYGME"
                     /name="site-specific DNA-methyltransferase"
     gene            2088..4724
                     /locus_tag="K5635_RS24260"
                     /old_locus_tag="SEL4261_P2020"
     CDS             2088..4724
                     /locus_tag="K5635_RS24260"
                     /old_locus_tag="SEL4261_P2020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012443154.1"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA];
                     GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 -
                     hydrolase activity [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DEAD/DEAH box helicase family protein"
                     /protein_id="WP_052922173.1"
                     /translation="MAKKPKSVGSEKLLFNRLKQFDEPGLFHDNYQTPDYIQENLKDAL
                     RPYQHGALRYLHYTQRKRDDALLHYRHLLFHMATGAGKTMVMAGTILYLFKELGYQNFI
                     FFVHTDAIIQKTRENLLNPQSPKYLFSQELEIDGEKITIEPIETFPSIPERNTIYLKLS
                     TIHKMHDELNSYRENSITYEDLKEIPLVLLGDEAHHFNAGTKARGKSKTSPENEEQTWE
                     RTIENILNLRPDNRLFEFTATIDLANKDIGQKYRGKVVYQYDLKQFMSDGYSKKVMLLE
                     ANQNDSDKMLDAVLLSQYRKLTAADHGITGFKPVILFKSNKIAISKAKQEEFSQLIAAM
                     TPESVRRHLANKKLQLSSDTSIWHKVIQRYANSDLVTVTGQIQEDFNDFNLLNVNKSDL
                     LEENPVLLNTLEEVDNPVRAVFAVAKVNEGWDVLNLYDIVRISEQASSSKTSTDSEAQL
                     IGRGARYYPFIYDGQRSFTRRFDNSTKDLSVLEQLHYHTINEPAYIKTLHASLEQADID
                     VHQDGGGTIEHARLKEDFKKSAVYQAGKLYFNEVEEIESSSRNWETYSLETRFEIPYQT
                     VCEESLDNLTGTKTGITKPELLVLDERFYRKAMQRISFYALDNLQRFFPKLTGIREFIR
                     SDAYLGKLKITVIVPQSLDFTTVPAKDKLHLLETVLLRISENVRRNDQKVKGTYRFISQ
                     PVKEVIKDYSLHIDPSVVINQKITAAPTIGKKWYVYDNAILNQLEHRLIKTLEAFMPKL
                     KARYDDIYVLRNDEQSTRFKLTEFGGVRGFMPDFIMILTRHSDNTYWQVFLEPKGDDRL
                     LDDAWKERMLETLNDRERIVIDENEHVRLVGIKFFANSQMDVFVSDMQNKLNDGESLET
                     SSLSLPL"
                     /name="DEAD/DEAH box helicase family protein"
     gene            complement(5122..5235)
                     /locus_tag="K5635_RS24520"
     CDS             complement(5122..5235)
                     /locus_tag="K5635_RS24520"
                     /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_072071404.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLLPLAAATGN"
                     /name="replication initiation protein"
     gene            complement(5893..6084)
                     /locus_tag="K5635_RS24265"
                     /old_locus_tag="SEL4261_P2030"
     CDS             complement(5893..6084)
                     /locus_tag="K5635_RS24265"
                     /old_locus_tag="SEL4261_P2030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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_048228005.1"
                     /translation="MNKQQQTALNMARFIKSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFSDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          5731..5815
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.674"
                     /coverage="100.0"
                     /evalue="6.569999999999999e-34"
     Typing          6121..6209
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.703"
                     /coverage="91.0"
                     /evalue="2.27e-34"
     Typing          complement(5164..5711)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.128"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 catttccccg caactgcatc caactcatag ctgtcgggtt ccagcaccga acgctatacc
       61 ttacaatcat tccaatattt aacagtcata aggccatgac atgcagaccg aattaataaa
      121 agaacttaac aaggttttaa aagcattccc gcaattctgg aacggagagg aattacaacg
      181 ttcaatggtg agtgacgcta tcagtcaaaa gcagccagac cttatcaagg cattggtcga
      241 taatgaaaaa gtccgctctg tttatggtgc ggatattgat ggcattttta tctttgactt
      301 tgacaaatta tgtggtcttc taaaatacaa agaatattgg gctaatagct tcactaaata
      361 ccggaacaaa gtgggattaa ctagcgaagg taaatacctt gattacagtt ctgatgtggt
      421 gctggatttt cctttcaagg attgtgttct tgaaggtggt atgtcgaaag aagatcaagg
      481 aaaatcagag gtttactata atgaaatcat cgcgcgagat gaaatagatc atttgttctc
      541 accgaaagtt ctcaaagaag taaatcgtta ctctaaagaa ggagtaaaaa aagaaagaat
      601 atttaaccgt aatgataatt taattatcag aggaaataac ctaattgcgt tgcactgtat
      661 aaaaaatata tacgagaagt cagttaaatt aatttatata gatccaccat ataatactga
      721 tacagatagc tttaaatata atgataaatt tagtcactct acgtggctga ctttcatgaa
      781 gaacagactt gaagttgcaa aagatttgtt gtgcgatgac gggttaattg caattagtat
      841 tgatgataat gaattaaatt atttggcctc gttggctgat gatatttttg gccgaaaaaa
      901 taggattgct atattcccaa gaataacaaa gaaaggagga aaatccgcca gcattttcgc
      961 aaagaatcat gattacatac tgctttatgt tagaagttta gaaaacaagc gtatgtatgc
     1021 agtttcgcac gacgacgata atttcaaata taaagatgag tactttgctg agagaggaag
     1081 ctacaaactc aaccaaacct tggattatga tagccttcaa tacagcaaat cacttgatta
     1141 tataatagaa atcaatggtg agaaatatta cccaggtggt gatgaaaatt tatttaatga
     1201 tagaatgaat ggcaagcata acagggcgga ctgggcttgg agatggagta ggaaattatt
     1261 cgattttggg tttgaaaatg ggtttattga aataagaaat ggcggccaaa ggccaaggat
     1321 atatacaaaa acatatcaaa atgcaaagat atcaaaggac ggaaatgatt atgtcataac
     1381 ctactttgat agaacaaagc cattgtcaac acttgagttt actgaaaaca agtattctaa
     1441 cgacaatgcg acaaaacaca ttagctccct cttagggaaa aatatatttg attatacaaa
     1501 accagaaacc ctattggcta agctaatcga aataacatct actaaaaatg acctaattct
     1561 agactttaat cttggtagtg gaactacagc tgctgttgct cacaaaatgg ggcgtcgcta
     1621 tatcggtatt gagcagatgg agtacatcaa cgacattacg gtacctcgcc tgaaaaaagt
     1681 catcgaaggt gaacaggggg ggatctcaaa agacgttaac tggcaggggg gaggcagctt
     1741 tgtctacgca gaattgatgg agctgaacgc ctatttcgtg catgaaattc agaaagcgca
     1801 gtccacggaa gaactcgaaa aactctttac catgatgaaa acagaggccc atctcaacta
     1861 tcaggtagag ctggaaaatg tgctgtccgc tgagtacgaa gtggatggca tcttccgtaa
     1921 ggtagctttc agtgaactgg aactgcatga gcagaagcag cttctgattg aaatcctcga
     1981 taaaaataaa ctctacgtga atgtctctga tatggaggac agcgaactga gcatttcgga
     2041 gagcgataaa gcctttaccc gcagcttcta cggaatggag tgacggcatg gcgaagaaac
     2101 cgaagtcagt cggcagtgag aagctactgt ttaacaggct gaagcagttc gatgaaccag
     2161 gactgttcca cgataactat cagacgccgg actatattca ggaaaacctg aaagatgccc
     2221 tgcgccccta tcagcacggt gcactgcgtt acctgcatta cacgcaacgt aaacgggatg
     2281 atgcgctgct gcattatcgc cacctgctgt ttcacatggc aaccggtgca gggaaaacga
     2341 tggtgatggc aggaacgata ctttatctgt ttaaagagtt agggtatcag aacttcattt
     2401 tcttcgtgca tacagacgcg attatccaga aaacgcgaga gaacttgctt aatccgcaat
     2461 cgccgaagta cctgttcagt caggagctgg aaatcgacgg ggaaaaaatc accatcgaac
     2521 cgatagaaac attcccgtcc ataccggaac gtaacacgat ttacctcaag ctctctacta
     2581 tccataagat gcacgacgag ctgaacagct atcgtgagaa cagtatcacc tacgaggatt
     2641 taaaagaaat cccccttgtg ctgcttggtg acgaggcaca tcatttcaac gccggtacta
     2701 aagctagagg caagtcgaaa acctcaccgg agaacgagga gcagacctgg gaacgcacga
     2761 ttgagaacat cctcaacctg cgaccggata accgcctgtt cgagttcacc gccaccattg
     2821 accttgcgaa caaagatatc gggcagaaat accgtggtaa ggtggtgtat cagtatgacc
     2881 tgaaacagtt catgtcagac ggttactcga agaaagtcat gctgctggaa gccaaccaga
     2941 atgacagcga caagatgctt gatgcggtac ttttaagcca gtaccgtaaa ctgacggcag
     3001 cagatcacgg catcaccggc ttcaaaccgg tcattctgtt caagtcgaat aagattgcga
     3061 tatcaaaggc gaagcaggag gagttttcgc aactgatagc cgccatgaca cctgagagcg
     3121 tcagacgtca tctagctaac aaaaaactcc agctcagctc tgacaccagt atctggcata
     3181 aagtgattca gcgttacgct aacagtgatt tagtgacggt gactgggcaa attcaggagg
     3241 actttaacga ctttaacctg ctgaacgtca acaagtcaga tctgctggaa gagaatcccg
     3301 tcctgctgaa tacactagaa gaagtcgata atccggtgag agccgtcttt gccgtcgcga
     3361 aggtgaatga aggctgggac gttctcaacc tctacgatat tgtccgcatc agcgagcagg
     3421 cgagcagcag caaaaccagc acggacagcg aagcgcagct tatcgggcga ggcgcgcgtt
     3481 actacccgtt catttatgac ggtcaacgaa gcttcacccg ccgttttgat aacagtacga
     3541 aggatttgag cgtactggag caactgcact atcacaccat caatgaaccg gcgtacatca
     3601 aaacactgca tgcctctttg gagcaggcgg acattgatgt gcatcaggat ggcggcggta
     3661 cgattgaaca cgccagactg aaagaagatt ttaaaaagtc cgccgtgtat caggcgggta
     3721 agctgtactt caacgaagtg gaggagattg agagcagcag cagaaactgg gaaacctact
     3781 cgctggaaac acgctttgag ataccgtatc agaccgtctg cgaggagtcg ctggacaacc
     3841 tgacaggcac aaagactgga atcacaaaac cggaactact ggtactggac gagcgttttt
     3901 accgcaaggc gatgcaaagg atcagctttt acgcacttga taacctgcag cgtttcttcc
     3961 cgaaactgac aggcatccgt gagttcatcc gcagtgacgc ctatcttggt aagctgaaaa
     4021 ttacagtcat cgtaccgcag tcactggatt tcaccaccgt accggcaaaa gataagctgc
     4081 acctactgga aaccgttctg ctgcgtatct cagagaacgt tcgccgcaat gatcagaagg
     4141 taaaaggcac gtaccgcttt atcagccagc cggtgaaaga ggttattaaa gattacagtt
     4201 tgcacattga cccgtcggta gttattaatc agaaaatcac tgctgcaccc accattggta
     4261 aaaaatggta cgtgtacgat aatgcgatac tgaatcagct tgagcatcgc ctaattaaaa
     4321 cgctggaagc attcatgccg aagctaaaag cgcgttatga cgatatttac gtactgcgta
     4381 acgacgagca gtcaacgcgc tttaagctca cggagttcgg cggcgtgcgc gggtttatgc
     4441 cagatttcat catgatactg acgcgccatt cggacaacac ttactggcag gtgttccttg
     4501 aaccgaaggg ggatgatcgt ttgctggatg acgcatggaa agaacggatg ctcgaaaccc
     4561 tgaatgatag ggagcgcatt gtaattgatg aaaatgagca cgtcagactg gttgggatta
     4621 aattctttgc caacagccag atggacgttt ttgtcagcga catgcagaac aagctgaatg
     4681 atggagaatc gctcgaaacc tcctcgcttt ccctaccact gtaaatcacg acaataaata
     4741 acggagcatt acgctccgtt attttattgt tatccctaac cacctccccg ggagttgatg
     4801 attgctcctg taatggttgc attgtttgtt cttgctgttg cgaatcatta gttttgaatt
     4861 gtggttaaaa accgttcgct atgtttatgc ctagggggat gagggggaaa agattcaagg
     4921 atcctcttgt gatccttttt ttctgcgcgt aatctgctgc ctgtaaacga aaaaaccacc
     4981 ctggcaggtg gtttttcgaa ggttagctaa tcctggcaga ttatctaacc gggtaactgg
     5041 cttggaggag cgcagtcacc aaaatctgtt ctttcagttt agccttaaca ggtgcataac
     5101 ttcaagacaa actcctctaa atcagttacc agtggctgct gccagtggca ataagtcgtg
     5161 tcttaccggg ttggactcaa gacgatagtt accggataag gcgcagcggt cgggctgaac
     5221 ggggggttcg tgcacacagc ccagcttgga gcgaacgacc tacaccgaac tgagatacca
     5281 acagcgtgag ctatgagaaa gcgccacgct tcccgaaggg agaaaggcgg acaggtatcc
     5341 ggtaatcggc agggtcggaa caggagagcg cacgagggag ccaccagggg gaaactcctg
     5401 gtatctttaa gtcctgtcgg gtttcgccac ctctgacttg agcgtcgatt tttgtgatgc
     5461 tcgtcagggg ggcggagcct atggaaaaac gccatcggcg cggccttttc ttggttcttg
     5521 ttttttgctc acatgctcct tttggcttta tcccctgatt ctgtggatca ccgcattacc
     5581 gtttttgagt gggctgatac cgctcgccgc agccgaacgg ccgagcgtag cgagtcagtg
     5641 agcgaggaag cggaagagtg cctgaacagg catgttctcc ttacgcatct atgcgatatt
     5701 tcacaccgca tatgccgctg ttttcttaca atctgcactg attccgcaca gttaagccag
     5761 tatacactcc gctatcgcta cgtgactggt tcagggcttc gccccgaaac cccctgatgt
     5821 gccctgaagg gcttgtctgc ccccggcatc cgctcacagg caagctgtgg ccgtctccgg
     5881 gagctgtatg tgtcagaggt tttcaccatc atcactgaag cgagcgaggc aactgcggta
     5941 gagttcgtcg gcgtggtcgt gaagtgattc gcagatgtcc gcctgttcgt ccgcgtccag
     6001 ctcgttgagt ttttccagca gggttagcgt ctggcttttg ataaatcgcg ccatattcag
     6061 cgcagtttgt tgctgtttgt tcaccttcgg ttgttctccg tcagtaccgg gtgtcgggtg
     6121 gaccctgacc aggtggtaat tgtaagacgt tgcgcgcgac ggtattacaa ttgcacatcc
     6181 tgtcctgttt tttaggaggt atcatggcat atcaactgat aaataatccc tgtgctgtac
     6241 agccgctgtt gcataaaatt tcgctctgcg tcgaggtttt tttatcaaaa attccgcaga
     6301 taccccggaa aaacgcgagt ctgttctcat gcctgaaatg cccacacccc acgcaaaact
     6361 aattttttgc tgatttgctt ttgaaatcat gttgttatgg tttcaaaaat gtattttctt
     6421 tttcagattt atgcaaaagc acgtcgttga cgaccctatg gcgaccctac ttagggtcag
     6481 tactgacaat ctttataaaa aacagttaat taatgtatgg gcgtccctag gggcgcgtcg
     6541 cattttttta caggacaccc ctagcagcgc ccctaggggt gtctgctcag atatgcctgg
     6601 aattcacgta ctgaaaatgt ctgaaaatgt gccttattgg caccgaatgc actcaaaccg
     6661 atcgtcattc actttcatgc atagctatgc atcgagctga aaacgatcct gacgcatttt
     6721 tctggttttc actgggtaaa acatctcttt ttgcggtgtt tgcgtcagaa tcgcgttcag
     6781 cgcgttttag tggtgcgcgc aagagcgttt atgttaaata ccacccattc tgatg
//
