LOCUS       NZ_AP023298             4060 bp    DNA     circular CON 23-SEP-2023
DEFINITION  Salmonella enterica subsp. enterica serovar 4,[5],12:i:- strain
            L-4261 plasmid pSAL4261-4, complete sequence.
ACCESSION   NZ_AP023298
VERSION     NZ_AP023298.1
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  JOURNAL   Unpublished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 4060)
  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
            AP023298.1.
            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..4060
                     /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="pSAL4261-4"
                     /geo_loc_name="Japan"
                     /collection_date="2014"
     gene            101..802
                     /locus_tag="K5635_RS24295"
                     /old_locus_tag="SEL4261_P4010"
     CDS             101..802
                     /locus_tag="K5635_RS24295"
                     /old_locus_tag="SEL4261_P4010"
                     /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_015059933.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCIGRLKSGADAESPKL
                     QKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRAQY
                     AKGEARAQITFSDAVMPYLTQLQGQFTRVVIKNISRLSRSYSIRIYELLQQFRSTGERI
                     IALDDFRSMLDIEHKYQTYKSLNQQLLRPCIDELNKKSDLVVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(1048..3195)
                     /gene="mobQ"
                     /locus_tag="K5635_RS24300"
                     /old_locus_tag="SEL4261_P4020"
     CDS             complement(1048..3195)
                     /gene="mobQ"
                     /locus_tag="K5635_RS24300"
                     /old_locus_tag="SEL4261_P4020"
                     /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_015059934.1"
                     /translation="MAIYHLSMKIISRNSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPHELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNGGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPKDSN
                     SAWKLTSNAMSMMADMQATRRRWEELNTERKVAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQMAFEKQWQKWGESGLAALRAQL
                     LKREEELRRKEQEDTERSRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRARIFERVDLMRDRSGYICDRSEIGQRPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKGLRYA
                     GYGVAVNHDADSHISPAPELMQFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRTWDEW
                     RREEDARTHATVRRHDRGWSQ"
                     /name="mobQ"
     gene            3374..3628
                     /gene="mobC"
                     /locus_tag="K5635_RS24305"
                     /old_locus_tag="SEL4261_P4030"
     CDS             3374..3628
                     /gene="mobC"
                     /locus_tag="K5635_RS24305"
                     /old_locus_tag="SEL4261_P4030"
                     /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_000091744.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     Typing          complement(2838..3196)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.444"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3197..3373
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          102..801
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(1052..3282)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.326"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gtaatattca cagaaaaagg gatattaaaa taaaaaggca ttgcctttcg ctgggggtat
       61 gtttatcttt tattcattac cttttgggga gggatgctct atgtcggatc taattgccta
      121 taaatctaat gcgctggttg aagccagtta taaattgacc ctacaggaac agcgattttt
      181 gttactttgc atcggtcgat tgaagtctgg ggctgatgca gaatctccaa aattgcaaaa
      241 gacaatgacc attacagctg cggaatattt cgattcattc cctgacatgg ggcggaaaaa
      301 tgccgaggtt cagttacagg aagcaattga tcgtttgtgg gacaggtcaa tcattctcaa
      361 ggatgacgag aaacgtgagg agttccgctg gatccagtat cgggcacagt acgctaaagg
      421 cgaggccaga gcacaaataa cattttctga cgcagtaatg ccttatttga cacaactaca
      481 agggcaattt actagagttg taatcaagaa tatatctaga ttatcaagaa gttacagtat
      541 aaggatatac gaactcctcc agcagttccg cagtactggc gaacgtatta tcgctctcga
      601 tgattttcgc tcaatgcttg atatagagca taaatatcaa acatataaat cacttaacca
      661 gcaattatta agaccctgca ttgacgaact gaacaaaaaa agcgatctgg ttgtaacggt
      721 tgagacgatc aaaaaggggc gcacggttgt agccctgcat tttcgcttca aggaagacaa
      781 acagatcaag atgacgatct agaatcgatt ttaaggcctc taaaacgttc tctggtgcgt
      841 ttttttggtg tcaggtatgc gatggtactg ctttggcaat aaattgcgtc agaattgatt
      901 tgagaggcca aaaaggaacc cccaattttg ggggcggaaa aacaaaacta tgtttgcgtt
      961 atgtgagtgt gcttcttgca ttcatccctg tcgatgaaca tcggcgaaca taacacgatg
     1021 ttacacaaaa caaaatattg ttcacattca ctgtgaccaa ccgcgatcat gtctcctcac
     1081 ggtggcgtgt gttcgtgcat cttcctcgcg ccgccattcg tcccaggtac gattaaaacc
     1141 cagcgagcgg aacagatgat ccggctgttt ttctggtgtg ttgacggcag caaaaagcgg
     1201 tgcctcacgg gttttcagat gaaactgcat cagttctggt gcaggtgata tgtggctgtc
     1261 tgcatcgtga tttacggcaa caccataccc tgcataccgt aaccccttat cggtcagtgc
     1321 actgatgacc agctggctgt tatcggctga gggaacggca aacgcgggat acagcgtacc
     1381 attaagccgg acaacaccgc ccagagagtc atccacgccc atgaccagca aaagctgaag
     1441 ttgtcgggtt tcccggtcta cagaactcat taccggcatc agcgtcggtg gcagacgtcc
     1501 ctgcgtaaaa tccaccttcc ttgctgccag tgatggcatg gctggctggc ggtcttctcc
     1561 aagacagaaa gactccggcc atgtcttcgg ctggcggaga ttgcgggtat gttgcggcca
     1621 tgtctggcaa acctgcgtca gcagttgctc aaaggtcgca gaggaataaa cacgttgcag
     1681 tggcggacgt tggccgattt cgcttcggtc acagatataa ccactcctgt cacgcattaa
     1741 atcaacacgc tcaaagattc tggcgcggta tttctccagt tcgttccccc agagcgtata
     1801 ttctccgttc cggttgtgaa gcagaaggta acaggtcatt tccccgttac caggcatggg
     1861 ggcctcgcca taccccgtaa cgactgcgct cagtacccct gaatccataa cggcattgtc
     1921 atttttcctg agctgctccg cgcgactacg ttcagtatct tcctgttcct tccggcgcaa
     1981 ttcctcttca cgtttaagca actgggctct gagagctgca aggccggatt ccccccactt
     2041 ctgccactgt ttttcaaatg ccatctgact cgcgggaatg tcctgtttct ccaccttccg
     2101 gtaatgctgt cgcaattttt ccatttgctg gctcagagac tggatttttc cctgctcact
     2161 acggtattcc ggtgccgccc attgcatcag gggaatacgg gaaaaaccgg acgaaaacgg
     2221 cgatgatttt ttcaggctgg cagcatggct catcgctacc tttcgttcgg tgttcagctc
     2281 ttcccagcgt ctgcgcgtcg cctgcatatc tgccatcatc gacatggcat tactggtgag
     2341 tttccatgcc gagttactgt ccttcggcaa cgcttcgatg atgtcacgta gtgtgtacga
     2401 agttgcgttg tcaggaagcc cgatattcag aaggtcagcc acacggcggg caggctctgt
     2461 cagccctccg ttcctgagtt cggtgcggga aatctgtatt tccaggttaa gcctgttaat
     2521 cagacgattc tgttcgccgc gttctgtttc gataccgcgt gtttccatcg cacaggcaga
     2581 ctttccgagg tgaataccag gcgttttctc aagcccctgt cgctcgtatg aacgatggtc
     2641 tatctcttcc tgataaccgg cgttcgccag tgccctgttt gcatggtcag cccatgatgc
     2701 ccgccacgtc tcggcatgtg tccggtcgtt ccagtccctg acctttccac cgaatccagc
     2761 aggtccgaca gctctcgtgg tcagcatgat gtgcgcatgg ggatttgttt tatccatgtg
     2821 atggaacgcc acatcagcaa tcatgccctg actgacaaag ttttctctga caaaggcgag
     2881 aacggtttcc cgtgcggcat cctgcggcag ttcgtggggg atggcgagtt caatttcccg
     2941 cgcaagttgt gagttcttcc ggcgttcggc cttctcaacg gcattccaga gttcggcacg
     3001 gttcgtacac caggcagggg ctgtcgcggg agtcagaatc acagcttcag ccacaccgct
     3061 tttgcgggtg tagtcgtgag tcagtccggt acgctcatca agcatcagtg aaccggaacg
     3121 ataggcagca gaagcaacgg cgctgtagcc gctgtttctg gagatgattt tcatgctgag
     3181 atgataaatc gccatttctg ccgtaatgcc tttttgtggt tttctttcag ccccgcaggg
     3241 cgcacacaat cgaaacggag tggagattgt ataagtgcgc acttcgtgat ttgccgtgca
     3301 ttatgccagc tcagttttta aactaccagt gacgcgctaa aatgcgattt ttcatcgcgc
     3361 acggagttac atcatgagca gaacactcga acagaagatt gctgatgctg aggccagatt
     3421 acagcgcctg aaggcgaaga gcaggagtct ggacacagcg cagaaggtca ttgtgggtgc
     3481 agcattgctg gcaaaggtca gaaagccgga ggaggtgcag ttgcgtgcct ggttactcca
     3541 gttcctgaag gcagaggtga cacgacaggc tgatgtgacg cgcatactgc cgctgattaa
     3601 cgagctggaa gcgctgccag aacagtgatt gtatcgtccg ctcgccgcag tcccagcgac
     3661 cgagcgttag cgagcgagtg ggcgaggaag cggaagtgaa tccgtcgcct gattgagcac
     3721 atacgcacgg tttttcggga ggtgatatgc gctgaacccg catgaatact ggatttccac
     3781 agggttggag ggggtgtatt cggaacttgc aattctgctt ttttgcaacg cattgttttt
     3841 attggttttt tgttttcagc actccaagtt atccacaggc tcgtcgttaa gtttttagat
     3901 cttgttttta agatcttgtt tttaatactt gttttagtgc caaaattcct tatagaaaac
     3961 aaaatgttac aacgctatag gtaatatgat ttaaggtaaa ggtaatatga tttaaggtgt
     4021 ttaggtaata tgatttaagg taaaggtaat atgatttaag
//
