LOCUS       NZ_AP028053             3530 bp    DNA     circular CON 21-JUN-2024
DEFINITION  Phytobacter diazotrophicus strain TA9832 plasmid pTMTA98323,
            complete sequence.
ACCESSION   NZ_AP028053
VERSION     NZ_AP028053.1
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  JOURNAL   Unpublished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 3530)
  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
            AP028053.1.
            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..3530
                     /organism="Phytobacter diazotrophicus"
                     /mol_type="genomic DNA"
                     /strain="TA9832"
                     /db_xref="taxon:395631"
                     /plasmid="pTMTA98323"
                     /geo_loc_name="Japan"
                     /collection_date="2020"
     gene            944..1090
                     /locus_tag="QUE83_RS29170"
     CDS             944..1090
                     /locus_tag="QUE83_RS29170"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001717510.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_063613191.1"
                     /translation="MHEPPVQSDRCALSGNYRLESNPERHDKTPLAAATGKRVYKRLLM
                     QSS"
                     /name="hypothetical protein"
     gene            complement(1314..2624)
                     /locus_tag="QUE83_RS29175"
                     /old_locus_tag="PDTA9832_57660"
     CDS             complement(1314..2624)
                     /locus_tag="QUE83_RS29175"
                     /old_locus_tag="PDTA9832_57660"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002437803.1"
                     /GO_process="GO:0006935 - chemotaxis [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="PAS domain-containing methyl-accepting chemotaxis
                     protein"
                     /protein_id="WP_237151429.1"
                     /translation="MYMRSLKNLFSLNRQRSAISYDAICQNKPVIEFSPEGVIHKASPL
                     FLSTMGYRADEIIGHHHRIFCPPSLVSSPEYSHFWQRLARGESFSGKFLRRAKGNRSVW
                     LEASYIPVTDRRGRVTRVIKIAADISERVHSALEQEAVLNAINRSMAIITFNPEGIVLD
                     ANENFVNATGYKRDEVIGKHHRLFCAETLYKSDEYRQFWERLNQGEFFSGQFPRINRQG
                     DPLWFRATYNPVFNSDGQLYKIVKFATDVTADVLRNQREQEAAVHAWDMAVQTRGSAQN
                     GANVIENSILMIDRIAQGMGAVSTDVSRLNNQSESIDGMVETIRKFAMQTRLIALNAAI
                     EAARAGASGRSFAVVAAEVRNLAASVSSATEEIEQVVASNSQLAKDVLSGIENSLMTTR
                     EGVTLMREAGEVMTSIQRNAAGVETAVKDVAISVKAG"
                     /name="PAS domain-containing methyl-accepting chemotaxis
                     protein"
     gene            3114..3281
                     /locus_tag="QUE83_RS29180"
                     /old_locus_tag="PDTA9832_57680"
     CDS             3114..3281
                     /locus_tag="QUE83_RS29180"
                     /old_locus_tag="PDTA9832_57680"
                     /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_154819077.1"
                     /translation="MQLKRKNPARAGKVFENIYMKAAIPAFLSKSVYDKKSAHGATREQ
                     GNYFLWWYWA"
                     /name="hypothetical protein"
     Typing          complement(410..583)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="93.75"
                     /coverage="100.0"
                     /evalue="5.6599999999999995e-68"
     Typing          complement(3366..3445)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="93.827"
                     /coverage="100.0"
                     /evalue="3.64e-26"
     Typing          507..1113
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.984"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atccataaca gcatcatgca acgacgacca ccgtccgtga cggccgcctc gtttaagtat
       61 ggacagaaat tcagaaaata ctcaggacga aatgtaatga atgcgaacgg attcaagaaa
      121 ttcgagcatg accgccctta cggccggtac ggtttcagac aaaatctgcc ggtatgcatc
      181 cagcatcatg gctcaggcat cccccccggc acgcctgagc cagcccgaaa caacgcgaca
      241 caagcaggtg tcgctcatca tcactaagag tcatcaggga tccggaagaa aaaccaaaca
      301 tggcttacct cctgttaacg gcaacacaga agaaattttt acagggtagc gggcaggaat
      361 gaaaaaaaat tgcagtcagg ccggaacggc tgctgaaccg gtacaggcgg gttccgggcg
      421 cagcgccgga ccagtcacgt agcgctagcg gagtgtatac tggcttaata tgttggcacg
      481 gatgcggatg tcagtgaagt gcttcatgtg gcaggagaaa gaaggcggca ccggcgcgtc
      541 agcagaatat gtaataacgg agatatgccg cttcctcgct cactgactcg ctgcgctcgg
      601 tcgttcggct gcggcgagcg gtaccggctt accggtgggg tggaaaattc ctagaagatg
      661 ccaggaagat acttagcgga acggagagaa ggctgcggcg aagccgtttt tccataggct
      721 ccgcccccct gacaagcatc acagaatctg acgctcaaat cagtggtggc gaaacccgac
      781 aggactataa agataccagg cgtttccccc tggtggctcc ctcgtgcgct ctcctgttcc
      841 tgcctttcgg tttaccggtg tcattccgct gttatggccg cggtttctca ttccacgcct
      901 gacactcggt tccgggaagg cagttcgctc caagctggac tgtatgcacg aaccccccgt
      961 tcagtccgac cgctgcgcct tatccggtaa ctatcgactt gagtccaacc cggaaagaca
     1021 cgacaaaacg ccactggcag cagccactgg taagagggtg tacaagagat tactgatgca
     1081 gagttcttga agtctcagcc caactacggc taaactggaa ggacgatttt ggtggcagcg
     1141 gtcttgtaca ccctgttacc acggttcata aacttgccgg tttaatgaac cttcgaaaaa
     1201 ccaccttgcc gggtggtttt ttcgttttca gagcaagaga ttacgacgca acggaaagga
     1261 tctcaagaag atcatctgtg atgttcgaca gatatgggga tatgcaccat ggcctatccg
     1321 gctttaactg aaatggcgac atccttaacc gcagtctcaa ctcctgcagc attcctctga
     1381 atgctggtca tcacttcacc cgcttcacgc atgagtgtga ccccttcccg ggtggtcatc
     1441 aggctgtttt caatgccact gagaacatct ttagccagtt gactattgct ggccacgact
     1501 tgctcaattt cttcagtcgc gctactgacg ctcgccgcaa gattacgcac ctctgcggca
     1561 acaaccgcaa aacttcttcc ggatgcgccc gcccttgctg cttcaatcgc ggcattcaat
     1621 gcaataagtc ttgtttgcat ggcaaacttc cggatggttt ccaccatacc gtcaatactt
     1681 tcagactgat tgttgagccg ggagacatcg gtggagacag ctcccatccc ctgcgcaatt
     1741 ctgtcaatca taaggatgct attttcaata acatttgcac cgttctgcgc acttcctcgt
     1801 gtctgcacgg ccatatccca tgcatgcaca gcagcctcct gctctctctg gtttcgcagg
     1861 acatcagccg tgacatctgt agcgaatttc acaattttat aaagctgccc gtcactgtta
     1921 aagacagggt tataagttgc acggaaccac agagggtctc cctgacggtt aatacgtgga
     1981 aactgaccag aaaaaaactc accctgattc agcctctccc agaactgtcg gtattcatca
     2041 cttttgtaaa gcgtctcggc acaaaacaga cgatgatgct taccgatgac ttcatcccgt
     2101 ttatagccag tggcattgac gaaattttca tttgcatcaa gcacgatccc ttcaggattg
     2161 aaggtgatta tggccataga acggtttatg gcatttagga ctgcttcctg ctcaagcgca
     2221 gaatgcacgc gctcagaaat atctgcagca attttaatga ctctggtcac acgaccgcgc
     2281 cggtcagtaa cggggatata actggcttca agccatacgg aacgatttcc ctttgcccgc
     2341 cgcaggaact tgccactaaa gctttctccc cgggcaaggc gctgccagaa atggctgtat
     2401 tccggtgaac tcaccagaga gggtgggcag aatatacgat ggtggtgacc gattatttca
     2461 tcagccctgt accccatagt ggagagaaaa agcgggctgg ctttatgtat caccccctct
     2521 ggactgaatt caatgacagg cttattctga caaattgcgt catacgaaat ggctgagcgc
     2581 tggcggttca gggagaacag atttttaagt gaacgcatat acatcagatt gctcggataa
     2641 tgtaaggact gccatggtta tccccgagga cgcggatacc atcatgcccg ccctgccggt
     2701 ggcagaaaaa aagctcccgg gcagggagcg gaagacaacg tgtcacagag ttaaaacctg
     2761 gtttcaggca cctcagttat cggccgccgc cgcgccggcc ttagagggca ggcggtaatt
     2821 ttttcgtcac gcgcttaagt tgcattgttc atgaaactta atgcaacagc ctgacgaatt
     2881 taccataaca tccgttgccc gcaccgccgc agaggtcctc agcgcgtttc tgacggcaga
     2941 acggtaaaac cagtaacaaa ccacccggaa aaccgccaga aacgcactgg aagtatttta
     3001 gcgctatgca tggctatgca cacaactgca tggcatgcag tttcgtccga aaagaacacg
     3061 ctaacccccg tttttagata ccgacaagga tgcgtgatac cagggagcct ggcatgcagc
     3121 taaaacgaaa aaacccggca cgggccggga aggtattcga aaatatttat atgaaagccg
     3181 ccattccggc attcttatcg aagagtgttt atgacaaaaa aagcgcacat ggggcaacaa
     3241 gagagcaggg aaactacttt ttatggtggt attgggcata agcctattct gttcgtggga
     3301 gaaagattat ctgaacagat aacggtgaac gggaacggat tttaatccgg cgtcgtgaag
     3361 cgttggcagg gtgtcgggga gcagccctga cctaagtatt tgtgatgccg gcgcgtgcgc
     3421 ggtattacaa atgcacatcc tgtccggagt ggttccccgg gaacaggcaa aaaaaaaacc
     3481 gggcgagctg cccggaaggt aagtcaagtt agattagatt acgttcactc
//
