LOCUS       NZ_CP047342             7081 bp    DNA     circular CON 01-APR-2024
DEFINITION  Proteus terrae subsp. cibarius strain ZF1 plasmid pZF1-7kb, complete
            sequence.
ACCESSION   NZ_CP047342
VERSION     NZ_CP047342.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13738032
            Assembly: GCF_011045795.1
KEYWORDS    RefSeq.
SOURCE      Proteus terrae subsp. cibarius
  ORGANISM  Proteus terrae subsp. cibarius
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Morganellaceae; Proteus.
REFERENCE   1  (bases 1 to 7081)
  AUTHORS   Peng,K. and Li,R.
  TITLE     The genomic epidemiology of tigecycline resistance gene tet(X)
            variants in a swine farm in China
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 7081)
  AUTHORS   Peng,K. and Li,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-JAN-2020) College of Veterinary Medicine, Yangzhou
            University, No. 567, Wenchang Middle Road, Hanjiang District, Yangz,
            Yangzhou, Jiangsu 225000, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 50.0x
            Sequencing Technology :: Oxford Nanopore MiniION; Illumina HiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_011045795.1-RS_2024_04_01
            Annotation Date                   :: 04/01/2024 03:57:49
            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)                     :: 4,042
            CDSs (total)                      :: 3,930
            Genes (coding)                    :: 3,881
            CDSs (with protein)               :: 3,881
            Genes (RNA)                       :: 112
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 49
            CDSs (without protein)            :: 49
            Pseudo Genes (ambiguous residues) :: 0 of 49
            Pseudo Genes (frameshifted)       :: 17 of 49
            Pseudo Genes (incomplete)         :: 29 of 49
            Pseudo Genes (internal stop)      :: 10 of 49
            Pseudo Genes (multiple problems)  :: 6 of 49
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP047342.1.
            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..7081
                     /organism="Proteus terrae subsp. cibarius"
                     /mol_type="genomic DNA"
                     /strain="ZF1"
                     /isolation_source="a feces sample of swine origin"
                     /sub_species="cibarius"
                     /db_xref="taxon:626774"
                     /plasmid="pZF1-7kb"
                     /geo_loc_name="China: Nantong, jiangsu province"
                     /lat_lon="31.41 N 120.11 E"
                     /collection_date="2018-05"
                     /collected_by="College of Veterinary Medicine, Yangzhou
                     University"
     gene            complement(join(6384..7081,1..1837))
                     /locus_tag="GTH23_RS20260"
                     /old_locus_tag="GTH23_20185"
     CDS             complement(join(6384..7081,1..1837))
                     /locus_tag="GTH23_RS20260"
                     /old_locus_tag="GTH23_20185"
                     /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="SIR2 family protein"
                     /protein_id="WP_165439383.1"
                     /translation="MENSELMKLKSLIGTQLESDLDLDKIERLILNGNAILFVGAGFSL
                     ESINVDGYKLPLAKDLAKIISKENSRYFQSIGADENYIKQVENCDDLMISSDIFLKEVP
                     QKNNLLNILKRTFSVKEVTDEQVSICKNSWRKIYTTNYDNAIELASLKSGKTITSLDLT
                     DDTGKYRRHKDICLHINGKIDGANERDLDNKIKLTTSSYLSSDQFLNSPWYSQFKNDIE
                     HCSAIFFVGYSMYDLDVQKILFNNKGIKSKTFFITRENSSKFDNYKLSIFGNILNIGIN
                     GFSKILNELSNDGKKEVEIVSSMEMYQNQLDNYEIRDFDISKFMLFGNVSNHYIDQCTL
                     TNDYDRRFIYRKEIEEIKNNILSGDNVIITSDLGNGKTILVKILMSIMTRVGFNCYLYS
                     SNEYSFTKDIEILSNNKNKNIIFIDNYDNSIDELKYILEQSHENIQVVITARHYGYENT
                     KELLLPIGLNKFKNYNLDYLLDDEVDSFINIVDNLGAWGDKAGLSKKRKLHGLDDEAKK
                     QLSILLLSVLESESIKTKINEITNNIFKNKGYKETIFAILLIDIIGHNMDRSIISDMAM
                     NNVIFSTDFIENKGVINLFRIEKGLIKTRSSTLSRFLISNQFEPMYIANQLLEIVNNLN
                     KNSSDTKDSSWQKIIKSLLRFSIVEKVLPQKRSAIKFYYEKLKVIIPRLIKEPHYWVQY
                     AMSVIPFKDYPNASIYLETAYSLAELKGSEYHTNNINTQQARLFFLKGLECKGAESFDL
                     FTKGDSLMQIIPNDIFKYRQISLYITFYEKVYATFNKGQKVEYERALKKIIKDSESRDL
                     ENGIYKSGDKWIEETIEKMNNILNIIENNRKK"
                     /name="SIR2 family protein"
     gene            2127..2363
                     /locus_tag="GTH23_RS20265"
                     /old_locus_tag="GTH23_20190"
     CDS             2127..2363
                     /locus_tag="GTH23_RS20265"
                     /old_locus_tag="GTH23_20190"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001159442.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_156734545.1"
                     /translation="MQFFTAHEVIIISAKYCDRCHLHAEKDDPEFHEFLSIDRQAGFGS
                     TFGDGNNLKLDLCQHCVKELLNPWLSVSEPDSF"
                     /name="hypothetical protein"
     gene            4130..4828
                     /locus_tag="GTH23_RS20270"
                     /old_locus_tag="GTH23_20195"
     CDS             4130..4828
                     /locus_tag="GTH23_RS20270"
                     /old_locus_tag="GTH23_20195"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_069368824.1"
                     /translation="MSELIAYKSNALIEASYKLTLQEQRLLLMCIGKLNPRDKTPQKTF
                     KITSGDFYLAFPDMGKSNAERHLKEAIDKLAERWIYIQNNNERRRIRWIQEEAEYFEGE
                     GKIEIVFADSIMPYLTQLQGQFTKIVIKNVSTLKSVYSIRLYELLMQFKVIGDRLISID
                     DFRSMLGLDEKKYATFKSLNQWVIKPAIKELNQKSNLSVTVDTVKKGRSVFALHFHFKE
                     DQQIKMMLED"
                     /name="replication initiation protein"
     gene            4831..5259
                     /locus_tag="GTH23_RS20275"
                     /old_locus_tag="GTH23_20200"
     CDS             4831..5259
                     /locus_tag="GTH23_RS20275"
                     /old_locus_tag="GTH23_20200"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006816427.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA-binding protein"
                     /protein_id="WP_164530221.1"
                     /translation="MALVSISEAARLTGKARSTLHKYIKQGRLSTTTDQNTGKKTIETS
                     ELIRVFGKISNLPTTISDSITSVSKLQPETQNDTQSLQAKLQLLEQENTHLKAEKELLS
                     KNLDDIRQAMLLIESKLPTTPEPVAPVPTKKPWQFWKK"
                     /name="DNA-binding protein"
     gene            5858..6082
                     /locus_tag="GTH23_RS20280"
                     /old_locus_tag="GTH23_20205"
     CDS             5858..6082
                     /locus_tag="GTH23_RS20280"
                     /old_locus_tag="GTH23_20205"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000879771.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF6290 family protein"
                     /protein_id="WP_156734551.1"
                     /translation="MLAIRLSDDIETRLESLAKQTGRTKTFYAREAILTHLEDLEDYYL
                     SAETVAKIRRGEELVHSSEDVRKALGLDD"
                     /name="DUF6290 family protein"
     gene            6066..6332
                     /locus_tag="GTH23_RS20285"
                     /old_locus_tag="GTH23_20210"
     CDS             6066..6332
                     /locus_tag="GTH23_RS20285"
                     /old_locus_tag="GTH23_20210"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000262326.1"
                     /GO_function="GO:0008657 - DNA topoisomerase type II
                     (double strand cut, ATP-hydrolyzing) inhibitor activity
                     [Evidence IEA]; GO:0042803 - protein homodimerization
                     activity [Evidence IEA]"
                     /GO_process="GO:0030541 - plasmid partitioning [Evidence
                     IEA]; GO:0051290 - protein heterotetramerization [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_156734549.1"
                     /translation="MVWTINYSERALKSLRKMDKQNARRIVDFMDLRIAVSDDPRQSGK
                     PLKGELGEFWRYRVGDYRILCQIIDDELIILAATIGHRKEVYL"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     Typing          4131..4828
                     /name="rep_cluster_1791"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aaaaccttga tagagtactt gaccttgttt ttattaagcc tttttcaatt ctaaataaat
       61 tgataactcc tttattttca atgaaatcag ttgaaaaaat cacattattc attgccatat
      121 ctgaaattat agaacggtcc atattatgac caataatatc aattaataaa attgcaaaaa
      181 tagtttcctt atatccttta tttttaaata tattattagt tatctcattt atttttgttt
      241 ttattgattc tgactccaat actgaaagca ataatattga caattgtttt tttgcttcat
      301 catctagccc gtgtagcttt ctcttcttag ataaaccggc cttatccccc caagctccca
      361 aattatcaac tatattgata aaactatcaa cctcatcatc taacaagtaa tccaaattat
      421 agtttttaaa tttatttagc cctatcggaa gtaatagctc ctttgtattt tcatacccat
      481 aatgtcgagc agtaattaca acttgtatat tttcatgaga ctgttcaagt atatatttga
      541 gttcatcaat agaattgtcg taattatcaa taaaaattat attcttattt ttattatttg
      601 ataaaatctc aatatcttta gtaaaagaat attcattact tgaatataaa taacaattaa
      661 acccgactct tgtcattatt gacattaata tttttacaag tatcgtcttc ccattaccta
      721 agtcacttgt aatgataaca ttatcgccag ataaaatatt attttttatt tcttcgattt
      781 cttttctata gataaatcta cgatcataat catttgtcaa agtgcactga tcaatataat
      841 ggttacttac attaccaaat aacataaatt tcgatatatc aaaatctctt atttcatagt
      901 tatctaattg attctgatac atttccatag aactaacaat ttcaacttct tttttcccat
      961 catttgataa ttcatttaat attttcgaga aaccattaat tcctatattt aatatattac
     1021 caaatataga taacttataa ttatcaaatt tactagaatt ttctctagtt atgaaaaatg
     1081 ttttactttt aattccctta ttattaaaga gtattttttg cacatctaaa tcatacattg
     1141 aatagccaac aaaaaaaata gcactgcaat gctctatatc attcttaaat tgagaatacc
     1201 atggtgaatt taaaaattgg tcagatgata agtatgacga tgttgttaat tttattttat
     1261 tatctagatc tctttcatta gcgccgtcta tttttccatt tatatgcaaa catatatctt
     1321 tatgtcttct atattttccc gtatcatcag ttaaatctaa agacgtaata gtctttccac
     1381 tttttaagct agctaattca attgcattat cataatttgt tgtatatatt tttctccaac
     1441 tatttttaca gatagacact tgttcatcag ttacttcttt aacggaaaaa gttcttttta
     1501 aaatatttaa taaattattt ttttgtggta cttcttttaa aaagatatca gagctaatca
     1561 ttaggtcatc acaattttcc acctgcttaa tataattttc atcagctcct atgctttgaa
     1621 aatatctaga attttctttt gaaattatct ttgccaaatc ttttgccaat ggcaatttat
     1681 aaccatcaac attaatagac tctaacgaaa aaccagcccc tacaaataaa atagcatttc
     1741 catttaaaat taatctttca attttatcta aatctaaatc actttctaac tgagtaccaa
     1801 taagtgattt aagtttcatc agttcactat tttccatttc acaatccatt aattaaatta
     1861 aaaatgatat ttttaaaaaa atattaatta catacaaaaa tatcccataa aacgcttatt
     1921 gtagcctggc gctttctgtt cctgaatagg ctactctcgt agttagagta ggaaaaccat
     1981 aaatactgta gataaactaa gtgaaaaata cagcaaaata tgttggaaat gtgcatcaat
     2041 tactagatat cagatggata ttattaaaaa aaacaataac atagttatat tgaatagaga
     2101 ttacactgac atcaaataga ggtcatatgc aatttttcac tgcgcacgaa gttatcatta
     2161 tttccgccaa atattgtgac agatgtcatt tgcacgctga aaaagacgat cctgaatttc
     2221 atgaatttct gtcgattgat cggcaggctg gttttggatc taccttcggt gatggaaata
     2281 acttgaagct ggatttatgt cagcattgcg tgaaagaact gttgaatccg tggttatcag
     2341 ttagtgaacc agattcattt tgacaatgaa agattgattt ttgaatccct taatcaacct
     2401 ttcaaattat aaataattga taattaatat ttttataaat tttacttctg ataaacacat
     2461 gcggaaaatc gttaaatttg gatacaaaaa aacgaaaatt aatcgcaatt aattgatttt
     2521 taatcattag cttacagtct ggtttaatgt attttcagcg aaaggttgat acatacaaga
     2581 tattccggct aaaaaacaac cgcacactta tcctcgtctt tttgatgaaa accagacttt
     2641 ttcatcagag atgtttgttt taaaaattat caaagacatt aagtcaccaa aaccctaatg
     2701 gtgacttaat gcataacgtt attaagtcac caagacccta gtgacgactt aatgtattgg
     2761 ctgtattaag tcactactag ggtagttacg gtataattag tttatgacca gacagggttt
     2821 taggctgggt taataacctt gtcattttcc ggtttacagg gggtactgtg agccgaaggc
     2881 gacgtagttt gtaccggtga ttaactgggt gaaattcctg atggattagt attgacgtca
     2941 agaatgaaga gagacaaaat caaattgcaa cgtttgtaga ctgccctgaa tggagatgaa
     3001 tatcctgttc ggggtttttg ccattttgat taatacaatc tcagaactat ggagtagacg
     3061 tcgaacctga acttagaacg tttaaaccga caaatgccag cacctgttct ggtctgaaaa
     3121 tgaaaaattg gtttttaaac tcagtaatga acctgttgcc ttgcagagaa caatctttta
     3181 gctgcatgtc ttacaaccgg caatctttag tttatccatt tgataaataa taatttaaat
     3241 aacattattc ttgctgttca aattctttca tcatcgtaaa taccaatatt catcggatat
     3301 caaaaacatc ataacctttt gatttaaaat gatctgaaat caaaatccag tgaaaggttg
     3361 acgtctgtgc ggcggattgc ttgattctta accaccttca ttcctgattc tgcatctgtt
     3421 cttttgaaaa aacagatttt gaaagtcaca tgaaccgttt tctgaacggc agcataaatt
     3481 ctgggaatat gcctgagaat gaaaaataca gtcttactgc aatatcggtt atagcaataa
     3541 aaagccacag aacgaatcag gagtggtttt tatatcttga atatggaatt catcgtcaca
     3601 agcgaagaaa gtcgcttata agctcataca gcactattct gattgagccg tgagcgtagc
     3661 gaacttaatt gcacggaaga atcagcggtt cagtggcttg atggtcggag acaaaaaata
     3721 ctgtcagcga tatgcccccg cattgcgggg gagctaccag ggtttgagaa tatgttttga
     3781 aaagaaataa acagagtttg cgacatcctt ttgaatacgg gaaaacgtga tgtatctgac
     3841 agattgagtt gatttatcca cagggctttt ctgttttaaa ttattttttg tttttaaatc
     3901 ttgttttatc tatgtatatc cttttgtttt ataagaatta aaaccctaat aggcatagaa
     3961 atttacggta ataggcatag aaatttacgg taataggcat agaaatttac ggtaataggc
     4021 atagaaattt acggtaatac tcacaaatta ggcatagata aaataaaaga cttgccttta
     4081 atgtagggat agactaattt tttgtctatc ccattgagta ggaagcgaca tgtctgaact
     4141 aatagcatat aaatccaatg cgttgattga agctagttac aaactaactt tacaggaaca
     4201 gcgcttgcta ttgatgtgta ttggaaagtt aaaccctcgg gataaaactc ctcaaaaaac
     4261 attcaaaatt acatctggcg atttttatct agcatttcct gatatgggaa aaagtaatgc
     4321 agaacgacat ttaaaagaag ctatagataa gctcgctgaa cgttggatat atatacaaaa
     4381 caataatgaa agacgacgta ttcgctggat ccaagaagaa gcagaatatt ttgagggtga
     4441 gggaaaaata gaaattgttt ttgctgactc cataatgccc tacttaactc agcttcaagg
     4501 tcaatttact aaaatcgtga tcaaaaatgt atcaacacta aaaagtgtct atagcattcg
     4561 tttatatgag ttattaatgc aatttaaagt gattggagat cgattgatca gcattgatga
     4621 ttttcgctcg atgctaggtt tggacgaaaa aaaatacgcc accttcaaat cacttaatca
     4681 gtgggtaata aaaccagcaa taaaagagtt aaaccaaaaa agcaatctat cagtaacagt
     4741 tgataccgta aaaaaaggca ggagtgtatt tgcactacac tttcacttca aagaagatca
     4801 acaaataaaa atgatgttag aggattgatt atggctttgg tatcaatcag tgaagcggca
     4861 agactgacag gaaaagcaag aagcacacta cacaagtata taaaacaagg aagactgtct
     4921 acgactacag atcagaatac tggtaaaaaa accattgaaa catctgaatt aattagagta
     4981 tttggcaaaa taagtaattt accaactaca atcagtgaca gcatcactag tgtatcaaaa
     5041 ctacaaccgg aaacacaaaa tgatacacag tcactacaag ctaaacttca actccttgaa
     5101 caagaaaata cacatttaaa agccgaaaaa gagctacttt caaaaaattt agatgacata
     5161 cgacaggcaa tgcttctaat tgaatccaag ctaccgacaa cacctgaacc cgttgcacca
     5221 gtaccaacaa aaaaaccgtg gcaattctgg aaaaaatagc cggttggtgt catttttacc
     5281 gcgaaaccga aaccgctatt gtgataacaa atgagtaaca ataaaacagt gtgttttcgg
     5341 caggaaaaga ggcggttttg aactgttcgg ggtgttttca ggatgaaacc agaagcgggt
     5401 gtgcgcttaa gcacgattat gttaaattat acacaatata ctgaatttaa cttacgccaa
     5461 gctttgtaaa ttgtaggatt gtatcttaca ttattcgctc attcattaat gtcagggtat
     5521 agataatata ccctgattgc ttcacttacc tgtggatttg ctcggtttta actcaggagt
     5581 atttcccgga gtatctttat tgtcgcgtcg acgttgatct ggttttcccg tcgattttgc
     5641 gatgggtttc ggaccaggtt taagacccat agtaatctcc tttctttgta agaggaaagc
     5701 cctcaatatg aacatatgag accgcattaa aaataatcaa gtcgggtaat atataaccac
     5761 attaatttct aacagaaaaa ggtgcttctg gtctttttca tagttttcga ctataatttg
     5821 ctatacatgt atagcaaaag tagatcaaga ggtagccatg ttagctattc gtttatctga
     5881 tgacattgaa acacgtctgg agtcactcgc aaaacagaca ggaagaacca aaacattcta
     5941 tgcgagagaa gctatcctca ctcatttgga agatttggaa gactactacc tttccgctga
     6001 aaccgttgca aaaattcgtc gcggtgaaga gttagttcat tcgtctgaag acgtgaggaa
     6061 agctcttggt ctggacgatt aattattctg aacgggcgtt aaaatctcta cgaaaaatgg
     6121 ataaacaaaa tgcgcgtcgt attgtagatt ttatggattt acgtattgca gtttcagatg
     6181 atcctcgaca gtcaggcaaa ccactcaaag gtgaactagg tgagttctgg cgttatagag
     6241 ttggtgatta tcggatacta tgccaaataa tagatgatga gcttatcatt cttgcagcta
     6301 ctatagggca ccgtaaagaa gtttatttat gattagcccg caatgcgagc tttctttaga
     6361 ctatagagcg ctgtagttaa atactatttt tttctattat tttctattat atttaatata
     6421 ttgttcattt tttctatagt ctcttctatc catttatctc cagatttata gataccattt
     6481 tcaagatctc tactttccga gtcttttatt attttcttta atgctctttc atattcaact
     6541 ttttgtcctt tattaaaggt agcatatacc ttttcataaa aagtaatata aagagatatt
     6601 tgcctatatt taaatatgtc atttgggatt atttgcatta aggaatcgcc tttagtaaat
     6661 agatcaaatg attcagctcc tttacattct aaccctttta aaaaaaacaa ccttgcttgc
     6721 tgggtattta tgttatttgt gtgatattca ctacctttaa gctctgctaa actatatgct
     6781 gtttccaagt aaattgaagc atttggataa tctttaaatg gtattactga cattgcatat
     6841 tgaacccagt aatgaggttc tttaatcaac ctaggaatga taactttaag tttttcataa
     6901 taaaatttaa ttgcacttct tttctgtggc aatacctttt caacgattga aaatctcaat
     6961 aaagacttta ttattttctg ccaactgcta tctttagtat cagagctgtt cttattaaga
     7021 ttattaacta tttccagtaa ttgattagct atatacatag gctcaaattg atttgaaatc
     7081 a
//
