LOCUS       NZ_AP025337             3530 bp    DNA     circular CON 13-MAR-2024
DEFINITION  Phytobacter diazotrophicus strain TA9734 plasmid pTMTA97343,
            complete sequence.
ACCESSION   NZ_AP025337
VERSION     NZ_AP025337.1
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  JOURNAL   Unpublished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 3530)
  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
            AP025337.1.
            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="TA9734"
                     /db_xref="taxon:395631"
                     /plasmid="pTMTA97343"
                     /geo_loc_name="Japan"
                     /collection_date="2020"
     gene            complement(134..301)
                     /locus_tag="L6445_RS29305"
                     /old_locus_tag="PDTA9734_58030"
     CDS             complement(134..301)
                     /locus_tag="L6445_RS29305"
                     /old_locus_tag="PDTA9734_58030"
                     /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"
     gene            791..2101
                     /locus_tag="L6445_RS29310"
                     /old_locus_tag="PDTA9734_58050"
     CDS             791..2101
                     /locus_tag="L6445_RS29310"
                     /old_locus_tag="PDTA9734_58050"
                     /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            complement(2325..2471)
                     /locus_tag="L6445_RS29315"
     CDS             complement(2325..2471)
                     /locus_tag="L6445_RS29315"
                     /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"
     Typing          2833..3003
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="94.22"
                     /coverage="98.0"
                     /evalue="5.6599999999999995e-68"
     Typing          complement(2303..2909)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.984"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gcgccggcat cacaaatact taggtcaggg ctgctccccg acaccctgcc aacgcttcac
       61 gacgccggat taaaatccgt tcccgttcac cgttatctgt tcagataatc tttctcccac
      121 gaacagaata ggcttatgcc caataccacc ataaaaagta gtttccctgc tctcttgttg
      181 ccccatgtgc gctttttttg tcataaacac tcttcgataa gaatgccgga atggcggctt
      241 tcatataaat attttcgaat accttcccgg cccgtgccgg gttttttcgt tttagctgca
      301 tgccaggctc cctggtatca cgcatccttg tcggtatcta aaaacggggg ttagcgtgtt
      361 cttttcggac gaaactgcat gccatgcagt tgtgtgcata gccatgcata gcgctaaaat
      421 acttccagtg cgtttctggc ggttttccgg gtggtttgtt actggtttta ccgttctgcc
      481 gtcagaaacg cgctgaggac ctctgcggcg gtgcgggcaa cggatgttat ggtaaattcg
      541 tcaggctgtt gcattaagtt tcatgaacaa tgcaacttaa gcgcgtgacg aaaaaattac
      601 cgcctgccct ctaaggccgg cgcggcggcg gccgataact gaggtgcctg aaaccaggtt
      661 ttaactctgt gacacgttgt cttccgctcc ctgcccggga gctttttttc tgccaccggc
      721 agggcgggca tgatggtatc cgcgtcctcg gggataacca tggcagtcct tacattatcc
      781 gagcaatctg atgtatatgc gttcacttaa aaatctgttc tccctgaacc gccagcgctc
      841 agccatttcg tatgacgcaa tttgtcagaa taagcctgtc attgaattca gtccagaggg
      901 ggtgatacat aaagccagcc cgctttttct ctccactatg gggtacaggg ctgatgaaat
      961 aatcggtcac caccatcgta tattctgccc accctctctg gtgagttcac cggaatacag
     1021 ccatttctgg cagcgccttg cccggggaga aagctttagt ggcaagttcc tgcggcgggc
     1081 aaagggaaat cgttccgtat ggcttgaagc cagttatatc cccgttactg accggcgcgg
     1141 tcgtgtgacc agagtcatta aaattgctgc agatatttct gagcgcgtgc attctgcgct
     1201 tgagcaggaa gcagtcctaa atgccataaa ccgttctatg gccataatca ccttcaatcc
     1261 tgaagggatc gtgcttgatg caaatgaaaa tttcgtcaat gccactggct ataaacggga
     1321 tgaagtcatc ggtaagcatc atcgtctgtt ttgtgccgag acgctttaca aaagtgatga
     1381 ataccgacag ttctgggaga ggctgaatca gggtgagttt ttttctggtc agtttccacg
     1441 tattaaccgt cagggagacc ctctgtggtt ccgtgcaact tataaccctg tctttaacag
     1501 tgacgggcag ctttataaaa ttgtgaaatt cgctacagat gtcacggctg atgtcctgcg
     1561 aaaccagaga gagcaggagg ctgctgtgca tgcatgggat atggccgtgc agacacgagg
     1621 aagtgcgcag aacggtgcaa atgttattga aaatagcatc cttatgattg acagaattgc
     1681 gcaggggatg ggagctgtct ccaccgatgt ctcccggctc aacaatcagt ctgaaagtat
     1741 tgacggtatg gtggaaacca tccggaagtt tgccatgcaa acaagactta ttgcattgaa
     1801 tgccgcgatt gaagcagcaa gggcgggcgc atccggaaga agttttgcgg ttgttgccgc
     1861 agaggtgcgt aatcttgcgg cgagcgtcag tagcgcgact gaagaaattg agcaagtcgt
     1921 ggccagcaat agtcaactgg ctaaagatgt tctcagtggc attgaaaaca gcctgatgac
     1981 cacccgggaa ggggtcacac tcatgcgtga agcgggtgaa gtgatgacca gcattcagag
     2041 gaatgctgca ggagttgaga ctgcggttaa ggatgtcgcc atttcagtta aagccggata
     2101 ggccatggtg catatcccca tatctgtcga acatcacaga tgatcttctt gagatccttt
     2161 ccgttgcgtc gtaatctctt gctctgaaaa cgaaaaaacc acccggcaag gtggtttttc
     2221 gaaggttcat taaaccggca agtttatgaa ccgtggtaac agggtgtaca agaccgctgc
     2281 caccaaaatc gtccttccag tttagccgta gttgggctga gacttcaaga actctgcatc
     2341 agtaatctct tgtacaccct cttaccagtg gctgctgcca gtggcgtttt gtcgtgtctt
     2401 tccgggttgg actcaagtcg atagttaccg gataaggcgc agcggtcgga ctgaacgggg
     2461 ggttcgtgca tacagtccag cttggagcga actgccttcc cggaaccgag tgtcaggcgt
     2521 ggaatgagaa accgcggcca taacagcgga atgacaccgg taaaccgaaa ggcaggaaca
     2581 ggagagcgca cgagggagcc accaggggga aacgcctggt atctttatag tcctgtcggg
     2641 tttcgccacc actgatttga gcgtcagatt ctgtgatgct tgtcaggggg gcggagccta
     2701 tggaaaaacg gcttcgccgc agccttctct ccgttccgct aagtatcttc ctggcatctt
     2761 ctaggaattt tccaccccac cggtaagccg gtaccgctcg ccgcagccga acgaccgagc
     2821 gcagcgagtc agtgagcgag gaagcggcat atctccgtta ttacatattc tgctgacgcg
     2881 ccggtgccgc cttctttctc ctgccacatg aagcacttca ctgacatccg catccgtgcc
     2941 aacatattaa gccagtatac actccgctag cgctacgtga ctggtccggc gctgcgcccg
     3001 gaacccgcct gtaccggttc agcagccgtt ccggcctgac tgcaattttt tttcattcct
     3061 gcccgctacc ctgtaaaaat ttcttctgtg ttgccgttaa caggaggtaa gccatgtttg
     3121 gtttttcttc cggatccctg atgactctta gtgatgatga gcgacacctg cttgtgtcgc
     3181 gttgtttcgg gctggctcag gcgtgccggg ggggatgcct gagccatgat gctggatgca
     3241 taccggcaga ttttgtctga aaccgtaccg gccgtaaggg cggtcatgct cgaatttctt
     3301 gaatccgttc gcattcatta catttcgtcc tgagtatttt ctgaatttct gtccatactt
     3361 aaacgaggcg gccgtcacgg acggtggtcg tcgttgcatg atgctgttat ggatgagtga
     3421 acgtaatcta atctaacttg acttaccttc cgggcagctc gcccggtttt ttttttgcct
     3481 gttcccgggg aaccactccg gacaggatgt gcatttgtaa taccgcgcac
//
