LOCUS       NZ_AP028045             3530 bp    DNA     circular CON 21-JUN-2024
DEFINITION  Phytobacter diazotrophicus strain TA9730 plasmid pTMTA97304,
            complete sequence.
ACCESSION   NZ_AP028045
VERSION     NZ_AP028045.1
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  JOURNAL   Unpublished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 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                   :: 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
            AP028045.1.
            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="TA9730"
                     /db_xref="taxon:395631"
                     /plasmid="pTMTA97304"
                     /geo_loc_name="Japan"
                     /collection_date="2020"
     gene            join(3486..3530,1..123)
                     /locus_tag="QUE90_RS29330"
     CDS             join(3486..3530,1..123)
                     /locus_tag="QUE90_RS29330"
                     /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            1316..1462
                     /locus_tag="QUE90_RS29335"
     CDS             1316..1462
                     /locus_tag="QUE90_RS29335"
                     /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(1686..2996)
                     /locus_tag="QUE90_RS29340"
                     /old_locus_tag="PDTA9730_57970"
     CDS             complement(1686..2996)
                     /locus_tag="QUE90_RS29340"
                     /old_locus_tag="PDTA9730_57970"
                     /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"
     Typing          complement(208..287)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="93.827"
                     /coverage="100.0"
                     /evalue="3.64e-26"
     Typing          complement(782..955)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="93.75"
                     /coverage="100.0"
                     /evalue="5.6599999999999995e-68"
     Typing          879..1485
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.984"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gaaaatattt atatgaaagc cgccattccg gcattcttat cgaagagtgt ttatgacaaa
       61 aaaagcgcac atggggcaac aagagagcag ggaaactact ttttatggtg gtattgggca
      121 taagcctatt ctgttcgtgg gagaaagatt atctgaacag ataacggtga acgggaacgg
      181 attttaatcc ggcgtcgtga agcgttggca gggtgtcggg gagcagccct gacctaagta
      241 tttgtgatgc cggcgcgtgc gcggtattac aaatgcacat cctgtccgga gtggttcccc
      301 gggaacaggc aaaaaaaaaa ccgggcgagc tgcccggaag gtaagtcaag ttagattaga
      361 ttacgttcac tcatccataa cagcatcatg caacgacgac caccgtccgt gacggccgcc
      421 tcgtttaagt atggacagaa attcagaaaa tactcaggac gaaatgtaat gaatgcgaac
      481 ggattcaaga aattcgagca tgaccgccct tacggccggt acggtttcag acaaaatctg
      541 ccggtatgca tccagcatca tggctcaggc atcccccccg gcacgcctga gccagcccga
      601 aacaacgcga cacaagcagg tgtcgctcat catcactaag agtcatcagg gatccggaag
      661 aaaaaccaaa catggcttac ctcctgttaa cggcaacaca gaagaaattt ttacagggta
      721 gcgggcagga atgaaaaaaa attgcagtca ggccggaacg gctgctgaac cggtacaggc
      781 gggttccggg cgcagcgccg gaccagtcac gtagcgctag cggagtgtat actggcttaa
      841 tatgttggca cggatgcgga tgtcagtgaa gtgcttcatg tggcaggaga aagaaggcgg
      901 caccggcgcg tcagcagaat atgtaataac ggagatatgc cgcttcctcg ctcactgact
      961 cgctgcgctc ggtcgttcgg ctgcggcgag cggtaccggc ttaccggtgg ggtggaaaat
     1021 tcctagaaga tgccaggaag atacttagcg gaacggagag aaggctgcgg cgaagccgtt
     1081 tttccatagg ctccgccccc ctgacaagca tcacagaatc tgacgctcaa atcagtggtg
     1141 gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggtggct ccctcgtgcg
     1201 ctctcctgtt cctgcctttc ggtttaccgg tgtcattccg ctgttatggc cgcggtttct
     1261 cattccacgc ctgacactcg gttccgggaa ggcagttcgc tccaagctgg actgtatgca
     1321 cgaacccccc gttcagtccg accgctgcgc cttatccggt aactatcgac ttgagtccaa
     1381 cccggaaaga cacgacaaaa cgccactggc agcagccact ggtaagaggg tgtacaagag
     1441 attactgatg cagagttctt gaagtctcag cccaactacg gctaaactgg aaggacgatt
     1501 ttggtggcag cggtcttgta caccctgtta ccacggttca taaacttgcc ggtttaatga
     1561 accttcgaaa aaccaccttg ccgggtggtt ttttcgtttt cagagcaaga gattacgacg
     1621 caacggaaag gatctcaaga agatcatctg tgatgttcga cagatatggg gatatgcacc
     1681 atggcctatc cggctttaac tgaaatggcg acatccttaa ccgcagtctc aactcctgca
     1741 gcattcctct gaatgctggt catcacttca cccgcttcac gcatgagtgt gaccccttcc
     1801 cgggtggtca tcaggctgtt ttcaatgcca ctgagaacat ctttagccag ttgactattg
     1861 ctggccacga cttgctcaat ttcttcagtc gcgctactga cgctcgccgc aagattacgc
     1921 acctctgcgg caacaaccgc aaaacttctt ccggatgcgc ccgcccttgc tgcttcaatc
     1981 gcggcattca atgcaataag tcttgtttgc atggcaaact tccggatggt ttccaccata
     2041 ccgtcaatac tttcagactg attgttgagc cgggagacat cggtggagac agctcccatc
     2101 ccctgcgcaa ttctgtcaat cataaggatg ctattttcaa taacatttgc accgttctgc
     2161 gcacttcctc gtgtctgcac ggccatatcc catgcatgca cagcagcctc ctgctctctc
     2221 tggtttcgca ggacatcagc cgtgacatct gtagcgaatt tcacaatttt ataaagctgc
     2281 ccgtcactgt taaagacagg gttataagtt gcacggaacc acagagggtc tccctgacgg
     2341 ttaatacgtg gaaactgacc agaaaaaaac tcaccctgat tcagcctctc ccagaactgt
     2401 cggtattcat cacttttgta aagcgtctcg gcacaaaaca gacgatgatg cttaccgatg
     2461 acttcatccc gtttatagcc agtggcattg acgaaatttt catttgcatc aagcacgatc
     2521 ccttcaggat tgaaggtgat tatggccata gaacggttta tggcatttag gactgcttcc
     2581 tgctcaagcg cagaatgcac gcgctcagaa atatctgcag caattttaat gactctggtc
     2641 acacgaccgc gccggtcagt aacggggata taactggctt caagccatac ggaacgattt
     2701 ccctttgccc gccgcaggaa cttgccacta aagctttctc cccgggcaag gcgctgccag
     2761 aaatggctgt attccggtga actcaccaga gagggtgggc agaatatacg atggtggtga
     2821 ccgattattt catcagccct gtaccccata gtggagagaa aaagcgggct ggctttatgt
     2881 atcaccccct ctggactgaa ttcaatgaca ggcttattct gacaaattgc gtcatacgaa
     2941 atggctgagc gctggcggtt cagggagaac agatttttaa gtgaacgcat atacatcaga
     3001 ttgctcggat aatgtaagga ctgccatggt tatccccgag gacgcggata ccatcatgcc
     3061 cgccctgccg gtggcagaaa aaaagctccc gggcagggag cggaagacaa cgtgtcacag
     3121 agttaaaacc tggtttcagg cacctcagtt atcggccgcc gccgcgccgg ccttagaggg
     3181 caggcggtaa ttttttcgtc acgcgcttaa gttgcattgt tcatgaaact taatgcaaca
     3241 gcctgacgaa tttaccataa catccgttgc ccgcaccgcc gcagaggtcc tcagcgcgtt
     3301 tctgacggca gaacggtaaa accagtaaca aaccacccgg aaaaccgcca gaaacgcact
     3361 ggaagtattt tagcgctatg catggctatg cacacaactg catggcatgc agtttcgtcc
     3421 gaaaagaaca cgctaacccc cgtttttaga taccgacaag gatgcgtgat accagggagc
     3481 ctggcatgca gctaaaacga aaaaacccgg cacgggccgg gaaggtattc
//
