LOCUS       NZ_AP028046             2496 bp    DNA     circular CON 21-JUN-2024
DEFINITION  Phytobacter diazotrophicus strain TA9730 plasmid pTMTA97305,
            complete sequence.
ACCESSION   NZ_AP028046
VERSION     NZ_AP028046.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00424021
            Sequence Read Archive: DRR328963, DRR328964
            Assembly: GCF_030296955.1
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 TA9730
  JOURNAL   Unpublished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                   :: 191x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030296955.1-RS_2024_06_21
            Annotation Date                   :: 06/21/2024 05:37:47
            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)                     :: 5,894
            CDSs (total)                      :: 5,775
            Genes (coding)                    :: 5,653
            CDSs (with protein)               :: 5,653
            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)              :: 122
            CDSs (without protein)            :: 122
            Pseudo Genes (ambiguous residues) :: 0 of 122
            Pseudo Genes (frameshifted)       :: 39 of 122
            Pseudo Genes (incomplete)         :: 87 of 122
            Pseudo Genes (internal stop)      :: 24 of 122
            Pseudo Genes (multiple problems)  :: 24 of 122
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP028046.1.
            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="TA9730"
                     /db_xref="taxon:395631"
                     /plasmid="pTMTA97305"
                     /geo_loc_name="Japan"
                     /collection_date="2020"
     gene            1007..1225
                     /locus_tag="QUE90_RS29345"
                     /old_locus_tag="PDTA9730_57990"
     CDS             1007..1225
                     /locus_tag="QUE90_RS29345"
                     /old_locus_tag="PDTA9730_57990"
                     /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"
     gene            complement(1523..1708)
                     /locus_tag="QUE90_RS29350"
                     /old_locus_tag="PDTA9730_58000"
     CDS             complement(1523..1708)
                     /locus_tag="QUE90_RS29350"
                     /old_locus_tag="PDTA9730_58000"
                     /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(2074..2301)
                     /locus_tag="QUE90_RS29355"
                     /old_locus_tag="PDTA9730_58010"
     CDS             complement(2074..2301)
                     /locus_tag="QUE90_RS29355"
                     /old_locus_tag="PDTA9730_58010"
                     /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"
     Typing          728..897
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="90.698"
                     /coverage="98.0"
                     /evalue="2.0600000000000002e-57"
     Typing          1389..1476
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="94.382"
                     /coverage="100.0"
                     /evalue="1.5000000000000001e-30"
     Typing          complement(221..803)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.331"
                     /coverage="97.0"
                     /evalue="0.0"
ORIGIN
        1 gtattcctct ttgtgaggtt ggatgtctaa tttataaagg atcttcttga gatccttttt
       61 tttcgcgcgt aatctcttgc cctgtaaacg aaaaaaccac cctggcaggt ggtttttcga
      121 aggttaggta atcctggcag atcccctaac cgtggtaaca gtcttgtgcg agacatgtca
      181 ccaaatttgt cctttcagtg tagcctcact aaggccgcca cttcaagaac tcttgataca
      241 tctctcgcac atcctgttta ccaatggccg ttgccaatgg cgattagtcg tgtctttccg
      301 ggttggactc aagttgatag ttaccggata aggcgcagcg gtcggactga acggggggtt
      361 cgtgcataca gtccatcctg gagcgaactg ccttcccgga actgagtgtc aggcgtggaa
      421 tgagaaaccg cggccataac agcggagtga caccggtaaa ccgaaaggca ggaatgcggg
      481 ggagcacgag ggagccacca gggggaaacg cctggtatct ttaagccgca tcgggtttcg
      541 ccaccactga tttgagcgtc agatttcgtg atgcttgtca ggggggcgga gcctatggaa
      601 aaacggcttt gccgtggcct tatgcctttt tcgctaagaa ccttcctggc attctccagg
      661 aaatttctgc tctgtacgta agcccgtacc gctcgccgca gccgaacgac cgagcgcagc
      721 gagtcagtga gcgaggaagc ggaatatctc ctgtatcaca tattctgctg acgcaccgat
      781 gccgcctttt tctcctgcca catgaagcac ttaactgaca tccgcatccg tgccaacata
      841 ttaagccagt atacactccg ctagcgctgc gtgactggtc cggcgctgcg cccggaaccc
      901 gcctgtaccg gttaagcagc cgttctggtc tgactgcgat ttttttcatt cctgcccgct
      961 accctgtaaa cctttcttct gcgttgccgt taacaggagg taagccatgt ttggtttttc
     1021 ctccggagcc ctgatgactt ttaatgatga tgagcgacac ctgcttgtgt ccgttgtttc
     1081 gggctggctc cggcgtgccg aaggggatgc cggagccatg atgctggatg cataccggca
     1141 gattttgtct gaaaccgaac cggccgcaag ggcggtcatg ctcgaatttc ttgaatcagt
     1201 tcgcattcat tacgtttcgt cctgagcatt tcctgaagca tttcctgaat ttttgtccat
     1261 actcaatcca ggcggccgtc acggacggtg gtcgtcgttc catgatgctg ttatggaaga
     1321 ttgagagtaa tctaacttga ttgagttccg ggcgtgtcgc ccggtttttt ttgctgtttc
     1381 ccggtgtccg ctcccggaca ggatgtgcat ttgtaatacc gcgcacgcgg cggcatcaca
     1441 aataccccgt tcagggctgc gccccgacac cccgccatcg cctcacggcc gcgcactgaa
     1501 ttgcgcaccc gttcaccgat tttcacgcat ctttctcgcc tatctgtgcg ttcagcatgg
     1561 cgtaaagcgc ttcagcctga tcgtgcagat gctcacagca gccggctgcc tcatccagat
     1621 ccatctgttc gagccgttcg aggaggagga gtgtctgtga gcggataaat ttggccatgt
     1681 tgagggcggc ggattcctgt ctggtcactg gtgattttcc ccgtctggtg atgatttttg
     1741 cgtgaaaaga gcatgccgtc attctggtgc atagtcatgc atgccgttaa aatttaacag
     1801 gcgcgtttct gacgggttcc ggggtggttt gttgtggttt ttgtcatggt tccgtcagaa
     1861 acgcgctgag cgcgtctgag gcggtgcggg caacggatgt tatggtaaat tcttgggggc
     1921 ttgattataa aataccgcac ttcctcttat gtcttgtgct ttttagacaa ccctgaaagc
     1981 ttttagcttt ggtgatgcaa tttgctggga ttttggcgga gaaccacagg taaagaaaaa
     2041 ggccacatta gcggcctttt tcggagaata tgctcagtgc ggaatttcgg agacttcttt
     2101 aacgtcggtt ttattgatct gctgtttgac accattcgcg tctgtatagc caagcaggcc
     2161 tgagtctgat tctttaggtt tgccgtcgct gacaatagtg cgaccgtcat tggtgtgtat
     2221 ggcatagctt gtgcgcgtgc agccggtgag ggctgaaagc gcaactgccg ctgcgaacac
     2281 tgaaacaaaa atctttttca aagccagctc cttttatcca tatcagtttt ggtcactaac
     2341 catctaacta taggttattt tttatgtgaa aagaggcttg atggtgggct gtatatcgag
     2401 ttaggcgcga ggtgctatgg tcaaagtgtg gtgtcaagcg gggaggaggc ttatatgaga
     2461 tgtaatccag cagatacata taccaagatg atttaa
//
