LOCUS       NZ_AP023297             4869 bp    DNA     circular CON 23-SEP-2023
DEFINITION  Salmonella enterica subsp. enterica serovar 4,[5],12:i:- strain
            L-4261 plasmid pSAL4261-3, complete sequence.
ACCESSION   NZ_AP023297
VERSION     NZ_AP023297.1
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  JOURNAL   Unpublished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 4869)
  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
            AP023297.1.
            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..4869
                     /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="pSAL4261-3"
                     /geo_loc_name="Japan"
                     /collection_date="2014"
     gene            101..1378
                     /gene="mobQ"
                     /locus_tag="K5635_RS24270"
                     /old_locus_tag="SEL4261_P3010"
     CDS             101..1378
                     /gene="mobQ"
                     /locus_tag="K5635_RS24270"
                     /old_locus_tag="SEL4261_P3010"
                     /inference="COORDINATES: protein motif:HMM:NF041496.1"
                     /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_221061099.1"
                     /translation="MAIYYFDVSNVSRSSGKKSASSVAAAAYQNRARYADERTGTTYDY
                     TKKGGLYYSGILAPENAPESLTASPLTLWNTVEATEKRKDARLAKDFKISLPIELSPEQ
                     NKALILDFAKQAFVSKGMIVDLAIHDIDTQPHSHIKTTTRELTPEGFGGKVREWDKKET
                     TLYWRELWAKVANEHLLKAGHDTTISHLTLKEQMKEALEEMDKTTDLEEKIKFASKAIE
                     LNRPAMKTISKKDWDDPKFQEIRKQEQEAKKQILKKAKNFRIKNTRELKEIQTELNKKF
                     RPSKIYKSVSEAIMNLNNKLTNSKLNNILNDKFDKLTKAIISIPENRKIKREKKIREKE
                     LEEEKRIFRETHKMDEFGNIYNIEDDKKWNKENNKLIKQQTASNKAKAEEERERKKLED
                     EANRLAEKNNISPNDFKQKKKKGLGI"
                     /name="mobQ"
     gene            complement(1406..1549)
                     /locus_tag="K5635_RS24275"
                     /old_locus_tag="SEL4261_P3020"
     CDS             complement(1406..1549)
                     /locus_tag="K5635_RS24275"
                     /old_locus_tag="SEL4261_P3020"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_159379050.1"
                     /translation="MKKKQKPKKRNRNKKSKFFKMLMASVREAVEISKGNIEPARITIL
                     KR"
                     /name="hypothetical protein"
     gene            complement(1549..2994)
                     /locus_tag="K5635_RS24280"
                     /old_locus_tag="SEL4261_P3030"
     CDS             complement(1549..2994)
                     /locus_tag="K5635_RS24280"
                     /old_locus_tag="SEL4261_P3030"
                     /inference="COORDINATES: protein motif:HMM:NF013603.3"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_221061100.1"
                     /translation="MFTGTSVFNKNRSVNRPDNLKEFASVNGERITERKKETFNIALSM
                     KSKGEDLQDETLTKRAERSLKCSSFRYIATVNGQAQTLYTHRCKGRHCQECQRIKAYIW
                     QKKTESIFPKLEENYLNAKYLFATFTIKNPKITDLRVVLSVMNKAANRLFKMKKYRDFI
                     LGGIRSTEITRGKSGADECHPHFHFLLMVKGNYGKKYYVNQEDWGKDWGDCLAYECDRV
                     GYPYNPVDYPRGFPIVDVVRAMDKEKKIEITNKNIKNSGEAIINYVLKYSVKGSDILDH
                     KKGKNDDWFFEFDKQIKGCRMITPVGVFKKYLSEIKKDPFDYDIEKAKIEERLGEGYQV
                     NKAIFKKGDYKLENKKDNEGYLLEALEAKAYNYQQLYLTMYSDYIKFYNDTNREISKLE
                     DKFFNEYDSMIESKIGRLLLIQEDRKKRINNTIESLKRVGYLKEEKGLYYDEWGSLWAT
                     FEIEKPTIEIVEINDFADMFEVW"
                     /name="protein rep"
     gene            complement(3873..4196)
                     /gene="traD"
                     /locus_tag="K5635_RS24285"
                     /old_locus_tag="SEL4261_P3040"
     CDS             complement(3873..4196)
                     /gene="traD"
                     /locus_tag="K5635_RS24285"
                     /old_locus_tag="SEL4261_P3040"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="conjugal transfer protein TraD"
                     /protein_id="WP_221061098.1"
                     /translation="MTTTTEKKYIKRTPEQRKAYLEAQLNSVNAKLNKQKRKEANAKRR
                     ETDHLKYTFAGDILKVIGCDVREVDLALVLGAVYYATNKNANSKNVELYRKAGLEILKE
                     NKK"
                     /name="traD"
     gene            complement(4405..4707)
                     /locus_tag="K5635_RS24290"
                     /old_locus_tag="SEL4261_P3060"
     CDS             complement(4405..4707)
                     /locus_tag="K5635_RS24290"
                     /old_locus_tag="SEL4261_P3060"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_119541917.1"
                     /translation="MSHDFYIERKKDKKKAVFNGYAEGVFYKHFHCEKYNAIWSGSNDG
                     KDISKKGTENALRKILESEEIKNYPDPDRINEIREFYENVVLKSNEQDKFYVHFL"
                     /name="hypothetical protein"
ORIGIN
        1 cgcattgcta acgcaatgac agggtttttt cccgtaaacg ggaaaaaaga aaagcaaaaa
       61 ccaaacccca aaaaaattag aaaagtggag gttttaaatt atggctatat attattttga
      121 tgtttccaat gtgagtagaa gctcaggcaa aaaatcagct tcgtctgttg ctgctgctgc
      181 ataccagaac agagccaggt acgcagacga acgaaccggt acaacctacg actacaccaa
      241 gaaggggggt ttatactact caggcatttt agccccggag aatgcaccag agagcctcac
      301 agcttcaccg ttgaccctat ggaacaccgt agaggctact gagaagagga aggatgccag
      361 gcttgccaaa gactttaaaa tctccctccc catagagcta tccccagaac agaacaaagc
      421 cctgatttta gactttgcaa aacaggcttt tgtatcaaag ggtatgattg tagatctggc
      481 tattcacgat atagacaccc aaccacatag ccatataaaa acaactacca gagaattaac
      541 accggaggga tttggtggaa aagttaggga atgggataaa aaagaaacga ctttatactg
      601 gagggaatta tgggcaaaag tggctaatga acatttatta aaagctggac acgatacaac
      661 tatcagccat ttgacattaa aagaacaaat gaaagaagca ctggaggaaa tggacaaaac
      721 aaccgacctg gaggaaaaaa taaaattcgc ttctaaggct atcgaattaa atagaccagc
      781 aatgaaaact atcagcaaaa aagactggga cgatcccaaa tttcaggaaa taagaaaaca
      841 ggaacaggag gcaaaaaaac aaatattaaa aaaggctaaa aattttagaa ttaaaaacac
      901 aagggaatta aaagaaatac aaacagaatt aaataaaaaa tttagaccgt cgaaaatata
      961 taaatcagta tcggaggcta ttatgaattt aaataataaa cttaccaatt caaaattaaa
     1021 taatatccta aatgataaat ttgataaact aacaaaagcc attatatcaa taccagaaaa
     1081 taggaaaata aagagggaga aaaaaataag agagaaggaa ttagaggaag aaaaaagaat
     1141 atttagagaa acccacaaaa tggatgagtt cggaaatatt tataatatag aggacgataa
     1201 aaaatggaat aaggaaaata ataaactgat taaacagcaa acagccagta ataaagcaaa
     1261 agccgaagaa gaaagagaga ggaaaaaatt agaggacgag gctaacagac tggctgaaaa
     1321 aaataatatt tcacctaacg actttaagca aaagaaaaag aaagggttag gtatataggg
     1381 ctatatacta caatatacta tactactatc tttttaaaat tgtgatcctt gctggctcaa
     1441 tatttccttt tgaaatttca acggcttcac gaaccgaagc cattagcatt ttaaagaatt
     1501 tactcttttt attacgattt ctttttttgg gcttctgttt ctttttcatt accacacctc
     1561 aaacatatca gcaaaatcgt taatctccac tatctcaata gtaggttttt caatttcaaa
     1621 tgttgcccaa agcgatcccc attcgtcata gtaaagccct ttttcttctt taagatagcc
     1681 gacccttttt aaactttcaa tagtgttatt aattcgtttt tttctatctt cctgaattaa
     1741 taataatctg ccaattttag actcgatcat actatcatat tcattaaaaa acttatcttc
     1801 taatttagat atttccctgt tagtgtcatt atagaactta atataatcac tatacatagt
     1861 taaatataat tgctgataat tatatgcttt tgcttccaat gcctctaata aataaccttc
     1921 attatctttt ttattttcaa gtttataatc gcctttttta aatatagctt tattaacctg
     1981 atagccttct cctaatcttt cctctatttt tgctttttca atatcataat caaacggatc
     2041 ttttttaatt tcgcttagat attttttaaa aactccaact ggtgttatca ttcgacaacc
     2101 tttaatttgc ttatcaaatt caaaaaacca atcgtcattt ttaccctttt tatggtctaa
     2161 aatatcactg cccttgacgg aatattttag aacataattt ataatcgctt cacccgaatt
     2221 tttaatattc ttattcgtta tttctatttt cttttctttg tccatagctc taacgacgtc
     2281 cacgattggg aacccacgag gataatcgac ggggttatac ggatacccta ccctatcaca
     2341 ctcataagcc aggcaatccc cccaatcctt cccccaatct tcctgattta catagtattt
     2401 tttaccgtaa ttgcctttta ccataagcaa aaaatgaaag tggggatggc attcgtctgc
     2461 cccagatttt ccccttgtga tctccgtcga acggatacct ccaagaataa aatctctata
     2521 ttttttcatt ttaaaaagtc tatttgctgc tttattcatt acagataaaa caacccttag
     2581 atctgttatt tttgggtttt taatcgtaaa tgtcgcaaat aaatattttg catttagata
     2641 gttttcttcc agttttggaa aaatagactc tgtttttttc tgccagatat aagccttaat
     2701 tctttggcat tcctgacagt ggcgaccttt gcaacggtga gtatataagg tttgagcctg
     2761 tccgttaaca gtagcgatat aacgaaaaga agaacacttt aaagaccttt cagccctttt
     2821 agttagtgtc tcgtcttgta gatcttcacc tttgcttttc atagacaaag caatattaaa
     2881 ggtctctttt tttctttctg ttattcgttc accgtttaca ctggcaaact cttttaaatt
     2941 atccggtcta ttgacagacc tatttttatt aaatacactt gtccctgtaa acatattaag
     3001 aaataccccg tattgtttga taccttcgca agttcaactc tacggggttt tttctttttg
     3061 tcaaaccagt caagcactta tcagatctac ctccaaaact tcccccaccg ccaaaagtcg
     3121 ataccgtccc attttttccg tgtttttatg ccgttacggt tagacccgtc ccatttttca
     3181 caccaaaaaa ccggtgttct aaatgttccg tcccaaatct tccgtttgtc ggatagtttt
     3241 aaaaggtgtc gtcccatttt ttggggtgtt ttctggcgat cttgaaggtg ctgtcccata
     3301 tcgggggaat tgattatttt ttgttctaaa attctttagc aaaaagtgct atttaccccc
     3361 cttgaaaact gctaaaaaaa tggggttaaa gccagtaatg acggggattg taggggagtt
     3421 ttagaagcca agttttgcct ccatttgttt cttactaaac aaggggaggg gttgcctctg
     3481 gcaaccttca aaccaaaccc ctcaaaccaa aggcaacccc taccggggca agttgtatta
     3541 tcaaatgtca tttaatacaa cttaaaacca tttaagggcg gcttatcagg tagaaggctc
     3601 actttgttca ccttccacct ttgccaagtg ttgtattgac cagggagccg tacaagcaca
     3661 atgacggaac cccagagggg accccccgac attctgcttg acggttcggc actggtgaac
     3721 ggtatcagaa aggacgaaag gctaacctaa gttagcctct ccaatatccc cattaatggg
     3781 gcaatttgcc gttatatata ttaaatttgt caaggaatta aataaacata ccgacttata
     3841 tataaataca atattattat atcttgtcaa acttattttt tattttcttt taaaatttcc
     3901 agtcctgctt ttctatatag ttcaacattt ttagaatttg cgtttttatt tgtagcatag
     3961 taaacagcac caagcaccaa agccagatca acttcccgaa cgtcgcaccc gataactttt
     4021 aaaatatcac ctgcaaaagt atattttaaa tgatccgttt ctcttctctt agcattagcc
     4081 tcttttcttt tctgcttgtt tagttttgca tttacactat taagctgggc ttctaaatat
     4141 gcctttcttt gctcaggagt tcttttaata tatttttttt cagtcgtcgt cgtcataata
     4201 tatatcctct tctaaatcaa aacccctctt attacattca ttaataacac aatctaattt
     4261 atactctaac cttaaaacaa gagattctaa accgtccgtt ttacctttga gtttttgata
     4321 attattaaaa aattcataca agaaacccat tataaggaca aaccccagac ctaaaagaaa
     4381 gcctataaaa atcataatct acccctataa aaaatgtaca tagaatttat cttgttcatt
     4441 cgattttaaa actacatttt cataaaattc tctaatttca ttaatacgat caggatctgg
     4501 gtagttctta atttcttccg actctaatat tttacgaagt gcattttcag tacctttttt
     4561 agaaatatct ttcccgtcat tactcccaga ccaaatagca ttatattttt cacaatgaaa
     4621 atgcttataa aacacaccct cagcatatcc attaaaaacg gctttctttt tatctttttt
     4681 tctttcgata taaaaatcat gcgacataaa aacctccata tatatttttg taattattaa
     4741 gcatatacct ccgtaattta ctttagtcaa atttatgtta tatctaaaat aaggaaaagc
     4801 atttttgccg ttctgaaagt tttttatttt gagtttacga aaaaataaaa attacttgaa
     4861 gcccttcta
//
