LOCUS       NZ_AP028054             2496 bp    DNA     circular CON 21-JUN-2024
DEFINITION  Phytobacter diazotrophicus strain TA9832 plasmid pTMTA98324,
            complete sequence.
ACCESSION   NZ_AP028054
VERSION     NZ_AP028054.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00424024
            Sequence Read Archive: DRR328969, DRR328970
            Assembly: GCF_030296995.1
KEYWORDS    RefSeq.
SOURCE      Phytobacter diazotrophicus
  ORGANISM  Phytobacter diazotrophicus
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Phytobacter.
REFERENCE   1
  AUTHORS   Kubota,H., Nakayama,Y. and Ariyoshi,T.
  TITLE     Complete genome sequence of Phytobacter diazotrophicus TA9832
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2496)
  AUTHORS   Kubota,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-APR-2023) Contact:Hiroaki Kubota Tokyo Metropolitan
            Institute of Public Health; 3-24-1 Hyakunincho, Tokyo 169-0073,
            Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Coverage                   :: 134x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030296995.1-RS_2024_06_21
            Annotation Date                   :: 06/21/2024 05:34:28
            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)                     :: 5,862
            CDSs (total)                      :: 5,743
            Genes (coding)                    :: 5,624
            CDSs (with protein)               :: 5,624
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 83
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 119
            CDSs (without protein)            :: 119
            Pseudo Genes (ambiguous residues) :: 0 of 119
            Pseudo Genes (frameshifted)       :: 40 of 119
            Pseudo Genes (incomplete)         :: 84 of 119
            Pseudo Genes (internal stop)      :: 24 of 119
            Pseudo Genes (multiple problems)  :: 24 of 119
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP028054.1.
            Annotated by DFAST https://dfast.ddbj.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..2496
                     /organism="Phytobacter diazotrophicus"
                     /mol_type="genomic DNA"
                     /strain="TA9832"
                     /db_xref="taxon:395631"
                     /plasmid="pTMTA98324"
                     /geo_loc_name="Japan"
                     /collection_date="2020"
     gene            complement(53..238)
                     /locus_tag="QUE83_RS29185"
                     /old_locus_tag="PDTA9832_57690"
     CDS             complement(53..238)
                     /locus_tag="QUE83_RS29185"
                     /old_locus_tag="PDTA9832_57690"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165998.1"
                     /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_032673404.1"
                     /translation="MTRQESAALNMAKFIRSQTLLLLERLEQMDLDEAAGCCEHLHDQA
                     EALYAMLNAQIGEKDA"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(604..831)
                     /locus_tag="QUE83_RS29190"
                     /old_locus_tag="PDTA9832_57700"
     CDS             complement(604..831)
                     /locus_tag="QUE83_RS29190"
                     /old_locus_tag="PDTA9832_57700"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010615788.1"
                     /GO_component="GO:0005886 - plasma membrane [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="YgdI/YgdR family lipoprotein"
                     /protein_id="WP_021243043.1"
                     /translation="MKKIFVSVFAAAVALSALTGCTRTSYAIHTNDGRTIVSDGKPKES
                     DSGLLGYTDANGVKQQINKTDVKEVSEIPH"
                     /name="YgdI/YgdR family lipoprotein"
     gene            2033..2251
                     /locus_tag="QUE83_RS29195"
                     /old_locus_tag="PDTA9832_57710"
     CDS             2033..2251
                     /locus_tag="QUE83_RS29195"
                     /old_locus_tag="PDTA9832_57710"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001046776.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_182407767.1"
                     /translation="MFGFSSGALMTFNDDERHLLVSVVSGWLRRAEGDAGAMMLDAYRQ
                     ILSETEPAARAVMLEFLESVRIHYVSS"
                     /name="hypothetical protein"
     Typing          1754..1923
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="90.698"
                     /coverage="98.0"
                     /evalue="2.0600000000000002e-57"
     Typing          2415..2496
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="93.976"
                     /coverage="93.0"
                     /evalue="3.2400000000000006e-27"
     Typing          complement(1247..1829)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.331"
                     /coverage="97.0"
                     /evalue="0.0"
ORIGIN
        1 cccgccatcg cctcacggcc gcgcactgaa ttgcgcaccc gttcaccgat tttcacgcat
       61 ctttctcgcc tatctgtgcg ttcagcatgg cgtaaagcgc ttcagcctga tcgtgcagat
      121 gctcacagca gccggctgcc tcatccagat ccatctgttc gagccgttcg aggaggagga
      181 gtgtctgtga gcggataaat ttggccatgt tgagggcggc ggattcctgt ctggtcactg
      241 gtgattttcc ccgtctggtg atgatttttg cgtgaaaaga gcatgccgtc attctggtgc
      301 atagtcatgc atgccgttaa aatttaacag gcgcgtttct gacgggttcc ggggtggttt
      361 gttgtggttt ttgtcatggt tccgtcagaa acgcgctgag cgcgtctgag gcggtgcggg
      421 caacggatgt tatggtaaat tcttgggggc ttgattataa aataccgcac ttcctcttat
      481 gtcttgtgct ttttagacaa ccctgaaagc ttttagcttt ggtgatgcaa tttgctggga
      541 ttttggcgga gaaccacagg taaagaaaaa ggccacatta gcggcctttt tcggagaata
      601 tgctcagtgc ggaatttcgg agacttcttt aacgtcggtt ttattgatct gctgtttgac
      661 accattcgcg tctgtatagc caagcaggcc tgagtctgat tctttaggtt tgccgtcgct
      721 gacaatagtg cgaccgtcat tggtgtgtat ggcatagctt gtgcgcgtgc agccggtgag
      781 ggctgaaagc gcaactgccg ctgcgaacac tgaaacaaaa atctttttca aagccagctc
      841 cttttatcca tatcagtttt ggtcactaac catctaacta taggttattt tttatgtgaa
      901 aagaggcttg atggtgggct gtatatcgag ttaggcgcga ggtgctatgg tcaaagtgtg
      961 gtgtcaagcg gggaggaggc ttatatgaga tgtaatccag cagatacata taccaagatg
     1021 atttaagtat tcctctttgt gaggttggat gtctaattta taaaggatct tcttgagatc
     1081 cttttttttc gcgcgtaatc tcttgccctg taaacgaaaa aaccaccctg gcaggtggtt
     1141 tttcgaaggt taggtaatcc tggcagatcc cctaaccgtg gtaacagtct tgtgcgagac
     1201 atgtcaccaa atttgtcctt tcagtgtagc ctcactaagg ccgccacttc aagaactctt
     1261 gatacatctc tcgcacatcc tgtttaccaa tggccgttgc caatggcgat tagtcgtgtc
     1321 tttccgggtt ggactcaagt tgatagttac cggataaggc gcagcggtcg gactgaacgg
     1381 ggggttcgtg catacagtcc atcctggagc gaactgcctt cccggaactg agtgtcaggc
     1441 gtggaatgag aaaccgcggc cataacagcg gagtgacacc ggtaaaccga aaggcaggaa
     1501 tgcgggggag cacgagggag ccaccagggg gaaacgcctg gtatctttaa gccgcatcgg
     1561 gtttcgccac cactgatttg agcgtcagat ttcgtgatgc ttgtcagggg ggcggagcct
     1621 atggaaaaac ggctttgccg tggccttatg cctttttcgc taagaacctt cctggcattc
     1681 tccaggaaat ttctgctctg tacgtaagcc cgtaccgctc gccgcagccg aacgaccgag
     1741 cgcagcgagt cagtgagcga ggaagcggaa tatctcctgt atcacatatt ctgctgacgc
     1801 accgatgccg cctttttctc ctgccacatg aagcacttaa ctgacatccg catccgtgcc
     1861 aacatattaa gccagtatac actccgctag cgctgcgtga ctggtccggc gctgcgcccg
     1921 gaacccgcct gtaccggtta agcagccgtt ctggtctgac tgcgattttt ttcattcctg
     1981 cccgctaccc tgtaaacctt tcttctgcgt tgccgttaac aggaggtaag ccatgtttgg
     2041 tttttcctcc ggagccctga tgacttttaa tgatgatgag cgacacctgc ttgtgtccgt
     2101 tgtttcgggc tggctccggc gtgccgaagg ggatgccgga gccatgatgc tggatgcata
     2161 ccggcagatt ttgtctgaaa ccgaaccggc cgcaagggcg gtcatgctcg aatttcttga
     2221 atcagttcgc attcattacg tttcgtcctg agcatttcct gaagcatttc ctgaattttt
     2281 gtccatactc aatccaggcg gccgtcacgg acggtggtcg tcgttccatg atgctgttat
     2341 ggaagattga gagtaatcta acttgattga gttccgggcg tgtcgcccgg ttttttttgc
     2401 tgtttcccgg tgtccgctcc cggacaggat gtgcatttgt aataccgcgc acgcggcggc
     2461 atcacaaata ccccgttcag ggctgcgccc cgacac
//
