LOCUS       NZ_AP025338             2496 bp    DNA     circular CON 13-MAR-2024
DEFINITION  Phytobacter diazotrophicus strain TA9734 plasmid pTMTA97344,
            complete sequence.
ACCESSION   NZ_AP025338
VERSION     NZ_AP025338.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00424022
            Sequence Read Archive: DRR328965, DRR328966
            Assembly: GCF_021654695.1
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 TA9734
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2496)
  AUTHORS   Kubota,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (07-DEC-2021) Contact:Hiroaki Kubota Tokyo Metropolitan
            Institute of Public Health; 3-24-1 Hyakunincho, Shinjuku-ku, Tokyo
            169-0073, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Coverage                   :: 98x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_021654695.1-RS_2024_03_13
            Annotation Date                   :: 03/13/2024 06:49:01
            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)                     :: 5,876
            CDSs (total)                      :: 5,758
            Genes (coding)                    :: 5,632
            CDSs (with protein)               :: 5,632
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 83
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 126
            CDSs (without protein)            :: 126
            Pseudo Genes (ambiguous residues) :: 0 of 126
            Pseudo Genes (frameshifted)       :: 44 of 126
            Pseudo Genes (incomplete)         :: 87 of 126
            Pseudo Genes (internal stop)      :: 25 of 126
            Pseudo Genes (multiple problems)  :: 26 of 126
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP025338.1.
            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="TA9734"
                     /db_xref="taxon:395631"
                     /plasmid="pTMTA97344"
                     /geo_loc_name="Japan"
                     /collection_date="2020"
     gene            join(2426..2496,1..157)
                     /locus_tag="L6445_RS29320"
     CDS             join(2426..2496,1..157)
                     /locus_tag="L6445_RS29320"
                     /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            523..708
                     /locus_tag="L6445_RS29325"
                     /old_locus_tag="PDTA9734_58070"
     CDS             523..708
                     /locus_tag="L6445_RS29325"
                     /old_locus_tag="PDTA9734_58070"
                     /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(1006..1224)
                     /locus_tag="L6445_RS29330"
                     /old_locus_tag="PDTA9734_58080"
     CDS             complement(1006..1224)
                     /locus_tag="L6445_RS29330"
                     /old_locus_tag="PDTA9734_58080"
                     /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          complement(756..843)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="94.382"
                     /coverage="100.0"
                     /evalue="1.5000000000000001e-30"
     Typing          complement(1332..1504)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="90.286"
                     /coverage="100.0"
                     /evalue="2.0600000000000002e-57"
     Typing          1429..2011
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.331"
                     /coverage="97.0"
                     /evalue="0.0"
ORIGIN
        1 aagctatgcc atacacacca atgacggtcg cactattgtc agcgacggca aacctaaaga
       61 atcagactca ggcctgcttg gctatacaga cgcgaatggt gtcaaacagc agatcaataa
      121 aaccgacgtt aaagaagtct ccgaaattcc gcactgagca tattctccga aaaaggccgc
      181 taatgtggcc tttttcttta cctgtggttc tccgccaaaa tcccagcaaa ttgcatcacc
      241 aaagctaaaa gctttcaggg ttgtctaaaa agcacaagac ataagaggaa gtgcggtatt
      301 ttataatcaa gcccccaaga atttaccata acatccgttg cccgcaccgc ctcagacgcg
      361 ctcagcgcgt ttctgacgga accatgacaa aaaccacaac aaaccacccc ggaacccgtc
      421 agaaacgcgc ctgttaaatt ttaacggcat gcatgactat gcaccagaat gacggcatgc
      481 tcttttcacg caaaaatcat caccagacgg ggaaaatcac cagtgaccag acaggaatcc
      541 gccgccctca acatggccaa atttatccgc tcacagacac tcctcctcct cgaacggctc
      601 gaacagatgg atctggatga ggcagccggc tgctgtgagc atctgcacga tcaggctgaa
      661 gcgctttacg ccatgctgaa cgcacagata ggcgagaaag atgcgtgaaa atcggtgaac
      721 gggtgcgcaa ttcagtgcgc ggccgtgagg cgatggcggg gtgtcggggc gcagccctga
      781 acggggtatt tgtgatgccg ccgcgtgcgc ggtattacaa atgcacatcc tgtccgggag
      841 cggacaccgg gaaacagcaa aaaaaaccgg gcgacacgcc cggaactcaa tcaagttaga
      901 ttactctcaa tcttccataa cagcatcatg gaacgacgac caccgtccgt gacggccgcc
      961 tggattgagt atggacaaaa attcaggaaa tgcttcagga aatgctcagg acgaaacgta
     1021 atgaatgcga actgattcaa gaaattcgag catgaccgcc cttgcggccg gttcggtttc
     1081 agacaaaatc tgccggtatg catccagcat catggctccg gcatcccctt cggcacgccg
     1141 gagccagccc gaaacaacgg acacaagcag gtgtcgctca tcatcattaa aagtcatcag
     1201 ggctccggag gaaaaaccaa acatggctta cctcctgtta acggcaacgc agaagaaagg
     1261 tttacagggt agcgggcagg aatgaaaaaa atcgcagtca gaccagaacg gctgcttaac
     1321 cggtacaggc gggttccggg cgcagcgccg gaccagtcac gcagcgctag cggagtgtat
     1381 actggcttaa tatgttggca cggatgcgga tgtcagttaa gtgcttcatg tggcaggaga
     1441 aaaaggcggc atcggtgcgt cagcagaata tgtgatacag gagatattcc gcttcctcgc
     1501 tcactgactc gctgcgctcg gtcgttcggc tgcggcgagc ggtacgggct tacgtacaga
     1561 gcagaaattt cctggagaat gccaggaagg ttcttagcga aaaaggcata aggccacggc
     1621 aaagccgttt ttccataggc tccgcccccc tgacaagcat cacgaaatct gacgctcaaa
     1681 tcagtggtgg cgaaacccga tgcggcttaa agataccagg cgtttccccc tggtggctcc
     1741 ctcgtgctcc cccgcattcc tgcctttcgg tttaccggtg tcactccgct gttatggccg
     1801 cggtttctca ttccacgcct gacactcagt tccgggaagg cagttcgctc caggatggac
     1861 tgtatgcacg aaccccccgt tcagtccgac cgctgcgcct tatccggtaa ctatcaactt
     1921 gagtccaacc cggaaagaca cgactaatcg ccattggcaa cggccattgg taaacaggat
     1981 gtgcgagaga tgtatcaaga gttcttgaag tggcggcctt agtgaggcta cactgaaagg
     2041 acaaatttgg tgacatgtct cgcacaagac tgttaccacg gttaggggat ctgccaggat
     2101 tacctaacct tcgaaaaacc acctgccagg gtggtttttt cgtttacagg gcaagagatt
     2161 acgcgcgaaa aaaaaggatc tcaagaagat cctttataaa ttagacatcc aacctcacaa
     2221 agaggaatac ttaaatcatc ttggtatatg tatctgctgg attacatctc atataagcct
     2281 cctccccgct tgacaccaca ctttgaccat agcacctcgc gcctaactcg atatacagcc
     2341 caccatcaag cctcttttca cataaaaaat aacctatagt tagatggtta gtgaccaaaa
     2401 ctgatatgga taaaaggagc tggctttgaa aaagattttt gtttcagtgt tcgcagcggc
     2461 agttgcgctt tcagccctca ccggctgcac gcgcac
//
