LOCUS       NZ_CP145146             5716 bp    DNA     circular CON 05-APR-2024
DEFINITION  Escherichia coli strain CAVp367 plasmid pCAVP367-5716, complete
            sequence.
ACCESSION   NZ_CP145146
VERSION     NZ_CP145146.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22837222
            Assembly: GCF_036785845.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5716)
  AUTHORS   Sheppard,A.E., Barry,K.E., Parikh,H.I., Vegesana,K., Sebra,R.,
            George,S., Sanderson,N.D., Stoesser,N., Eyre,D.W., Crook,D.W.,
            Walker,A.S. and Mathers,A.J.
  TITLE     Tn5403 promotes plasmid rearrangements and degradation of the
            Klebsiella pneumoniae carbapenemase (KPC) transposon Tn4401
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5716)
  AUTHORS   Sheppard,A.E., Barry,K.E., Parikh,H.I., Vegesana,K., Sebra,R.,
            George,S., Sanderson,N.D., Stoesser,N., Eyre,D.W., Crook,D.W.,
            Walker,A.S. and Mathers,A.J.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-FEB-2024) Biological Sciences, University of Adelaide,
            Victoria Drive, Adelaide 5005, Australia
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 369x and 93x
            Sequencing Technology             :: Oxford Nanopore and Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036785845.1-RS_2024_04_05
            Annotation Date                   :: 04/05/2024 15:59:11
            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)                     :: 5,333
            CDSs (total)                      :: 5,220
            Genes (coding)                    :: 4,992
            CDSs (with protein)               :: 4,992
            Genes (RNA)                       :: 113
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 228
            CDSs (without protein)            :: 228
            Pseudo Genes (ambiguous residues) :: 0 of 228
            Pseudo Genes (frameshifted)       :: 74 of 228
            Pseudo Genes (incomplete)         :: 172 of 228
            Pseudo Genes (internal stop)      :: 37 of 228
            Pseudo Genes (multiple problems)  :: 48 of 228
            Pseudo Genes (short protein)      :: 3 of 228
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP145146.1.
            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..5716
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="CAVp367"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pCAVP367-5716"
                     /geo_loc_name="USA:Virginia"
                     /lat_lon="38.14 N 78.45 W"
                     /collection_date="2017-02-01"
                     /collected_by="Clinical Microbiology University of Virginia
                     Health System"
     gene            join(4664..5716,1..33)
                     /locus_tag="LMH29_RS26625"
                     /old_locus_tag="LMH29_26625"
     CDS             join(4664..5716,1..33)
                     /locus_tag="LMH29_RS26625"
                     /old_locus_tag="LMH29_26625"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016230929.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_001530418.1"
                     /translation="MASYHCTVKTGAKGVALKHADYISRSGEYKNYKSREDLEFSSSGN
                     MPSWAKKNPAELWKAADEFERKNGTAYREIEIALPRELTREQRIELVEDFVQKELGDRH
                     AYQYAIHNPPGAIDGKEQPHAHIMFCERINDGIERDPQQFFKRANSKSPERGGAKKARF
                     GETPQERKSALVALRSHWADVQNEHLARHGHQSRVDHRSLKEQGIKRTPEVHLGPVRVA
                     VMNADQVCAILARRNAEREKLEAEQERDSIIDLKTTLKEALAERDNIPPSLDELGAELK
                     AFVESSFDELNEVMQLNSLINGALDSMMKQFQVEEERKLQQERLIEAEKQRDLERERER
                     VRQRAYSSPAPSRSRDYGMSR"
                     /name="MobA/MobL family protein"
     gene            54..770
                     /locus_tag="LMH29_RS26630"
                     /old_locus_tag="LMH29_26630"
     CDS             54..770
                     /locus_tag="LMH29_RS26630"
                     /old_locus_tag="LMH29_26630"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016235968.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001175444.1"
                     /translation="MQLDEHSRKIAALVAYNDKQIKEMNRLITLLNERVNDLNTFTSTL
                     EREGKVVSGISYSFRDSVSNVKFYINKGMDEASCKLQKSVSDTLTSLLREKLSFTLNDV
                     KKEWVDFEEQTSKEIKESLKQTTREAEVATGIIRKTMEKYTVTRIVEKVIVLIVLFLLL
                     MIAPVFYAEYLKMNISSLMEEQKKHESMLKEWKEKAPLAEFSKCGDYRKACVLVDDESG
                     YYFNEQSPNKKYAILK"
                     /name="hypothetical protein"
     gene            complement(828..1400)
                     /locus_tag="LMH29_RS26635"
                     /old_locus_tag="LMH29_26635"
     CDS             complement(828..1400)
                     /locus_tag="LMH29_RS26635"
                     /old_locus_tag="LMH29_26635"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001522465.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="LysE family translocator"
                     /protein_id="WP_000456846.1"
                     /translation="MEYSTLLSFAIVTLSQTISIGPGVALVINNAFSHGLKSSIKTSIY
                     IRIGETIVMAISLFALSSTSSTEQHFHIIKIFGGGYLIYIGLMGLINKKNKQRKEQKPF
                     LIPLLNPKAYLFFAALIPTFIDNNTNITLNFFILGVLFIFISFLTDLIYIAISLTIRDK
                     LTPSFSRYISICSSIFILGTGIYFIFT"
                     /name="LysE family translocator"
     gene            complement(1407..2357)
                     /locus_tag="LMH29_RS26640"
                     /old_locus_tag="LMH29_26640"
     CDS             complement(1407..2357)
                     /locus_tag="LMH29_RS26640"
                     /old_locus_tag="LMH29_26640"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001058673.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001058673.1"
                     /translation="MNNFINECISAPRINGMAEFFSSTASGEKHKPFRLVEIDDRLFHS
                     YDYIKFAKHLTKNSGPFVNHYFCSIPYSKEEECRLGTTVIKYAITLNKKLNTWCLGMAE
                     GAMARTISELSKGNIQTLTTSPTKENEHAFFKYGSSENAYFICTPFFLLEERLKNSNLK
                     QFNQGFDIIIEDTTFQMYSPNRSGQINHVKRLLNNDGIFIFTEKHSSEHDEYQKREIQK
                     DYSFKQRYFSKDEINTKKEIVLNTMNLNEVSVDDMLSAIKQHFKYASIYWNSGNFYSIA
                     ASNSLKHISTFINLLPKAAIPMEYVYEKLPRNISW"
                     /name="hypothetical protein"
     gene            2910..3839
                     /locus_tag="LMH29_RS26645"
                     /old_locus_tag="LMH29_26645"
     CDS             2910..3839
                     /locus_tag="LMH29_RS26645"
                     /old_locus_tag="LMH29_26645"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016237866.1"
                     /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_338544299.1"
                     /translation="MSAVLQLFREKLPHKPYCTNDFTYGVRILPKDIAILARFIQQNQP
                     HAQHWLAFDVDRTGAAIDWSDRNCPAPNITVKNPRNGHAHLLYALTLPVRTAPDASASA
                     LKYAAVIERALCEKLGADVNYSGLICKNPFHQEWQVVEWRWELYTLDELADYLDLSASA
                     RRRVDKDYGMGRNWYLFEKGRKWSYRAIRQGWPAFSPWLDAVIQRVEMYNASLPVPLSP
                     AECRAIGKSIAKYTYRKFSPEGFSAVQAARGRKGGNANSSENQAIKGQKSKRVAVGTSA
                     RTLKPWVTLGISRATYYRKLKCDPDLAK"
                     /name="replication initiation protein"
     gene            complement(4046..4492)
                     /locus_tag="LMH29_RS26650"
                     /old_locus_tag="LMH29_26650"
     CDS             complement(4046..4492)
                     /locus_tag="LMH29_RS26650"
                     /old_locus_tag="LMH29_26650"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000184721.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="conjugal transfer protein TraD"
                     /protein_id="WP_000184722.1"
                     /translation="MTNREEWLSAKIAYINGLKSPSEQQRLLVLLAEKKNRTTTDEKTL
                     SALIRAEKTAEKAAAAKARVTAIIAAERKAAARAERKARDHELYKAAGLMIVAGLVDSK
                     TGKPKFSAAELVGALAGIAELPRNHPKWQEWEKRGKELLTKDSA"
                     /name="conjugal transfer protein TraD"
     Typing          2911..3839
                     /name="rep_cluster_2141"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.398"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          4665..5686
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="94.0"
                     /evalue="0.0"
ORIGIN
        1 tcacgttcac gtgattatgg tatgagccgt taagcactgg aggtttttat tttatgcaat
       61 tggatgaaca ttcaagaaaa attgctgctc ttgttgcgta taatgataaa caaataaaag
      121 aaatgaacag gctaattact ctgcttaatg aaagagtgaa tgacttaaat acctttacaa
      181 gtactcttga acgtgaaggt aaagttgttt ctggaatttc ttattccttt agggatagtg
      241 tgtctaatgt taaattttat attaataaag gaatggatga ggcatcttgt aaattacaga
      301 aatcagtctc agatacacta acgtcattac tccgcgaaaa attatctttc actctcaatg
      361 atgtaaagaa agagtgggtt gatttcgagg agcaaacaag taaagagata aaggaatcat
      421 taaagcagac gaccagagag gccgaagttg cgacaggtat aattagaaaa acaatggaga
      481 agtatacagt aacaaggatt gtcgaaaagg taattgtgtt gattgtatta tttttattgc
      541 taatgatcgc tcctgttttc tatgctgaat atctcaaaat gaatattagt tcgctaatgg
      601 aagaacagaa aaaacatgaa tccatgttaa aagaatggaa agaaaaagct ccattggccg
      661 agttctcgaa gtgtggagat tatcgtaaag catgcgtgtt agttgatgac gaaagcggat
      721 attattttaa tgaacaatca ccaaataaaa aatatgccat actgaaatag tgttaagtaa
      781 ctcatgccgt cttatgacta aggctgcatg agtataaaaa cggcgtttca cgtaaaaata
      841 aaataaatac ctgtacctaa tataaaaatg gaactacata tgcttatgta tcttgagaat
      901 gatggcgtca atttatccct tatcgttaag ctaatagcta tgtaaataag atctgttagg
      961 aatgatataa atataaataa aacacccaat ataaaaaagt ttaatgtgat atttgtatta
     1021 ttatctataa aggttggtat taacgcagca aagaaaagat acgccttggg gtttaataat
     1081 ggtatcaaaa aaggtttttg ctcttttctt tgtttgtttt ttttattaat taaacccatt
     1141 aatcctatgt atattaaata gcctccaccg aatattttta taatgtgaaa atgttgttct
     1201 gtgctggatg ttgaggataa cgcgaaaaga gatattgcca tgacgatagt ctcgccaatt
     1261 cttatgtata tacttgtttt tattgatgac tttaatccat gtgaaaaggc attgtttata
     1321 accaatgcaa cgccaggccc tattgatata gtttgcgata aggttacgat agcaaatgat
     1381 aataatgttg aatattccat gtttacttac catgatatat ttcgtgggag cttttcatat
     1441 acatattcca taggaattgc agctttcggt aataaattta taaatgttga tatgtgtttt
     1501 agtgaattgc tggcggcgat tgagtaaaaa tttccgctat tccaatatat tgatgcgtat
     1561 ttaaaatgtt gtttaattgc ggaaagcata tcgtcaacac taacttcatt caaattcatt
     1621 gtgtttagta cgatttcctt tttggtgtta atctcatctt tcgagaaata cctttgtttg
     1681 aatgaataat ctttttggat ttctcttttt tgatattcat catgttctga actatgtttt
     1741 tctgtaaata tgaaaatacc atcattattt aatagccttt ttacgtggtt tatttgccca
     1801 gatctgttag gtgagtacat ttgaaatgtg gtgtcttcta ttataatatc gaatccttga
     1861 ttaaattgtt taagatttga attttttagt ctttcctcta acaggaaaaa tggagtgcaa
     1921 ataaaataag cgttttcact tgagccatac ttaaaaaatg catgttcatt ttcttttgtt
     1981 ggactggttg ttaatgtttg tatgtttcct tttgataatt ctgaaatggt tcttgccatt
     2041 gcgccctcag ccataccaag acaccatgtg tttaattttt tgtttagcgt gattgcgtat
     2101 tttattactg ttgttcctaa tctgcactct tcttccttgc tgtatggtat actgcaaaaa
     2161 taatgattaa cgaaagggcc gctgtttttt gtgaggtgtt tggcaaactt aatgtaatca
     2221 taagaatgaa aaagccgatc atctatttct actagtctaa aaggtttgtg tttttcccct
     2281 gatgcagttg atgagaaaaa ttctgccatg ccgtttattc tcggagcgga aatacattca
     2341 tttataaaat tattcatttt cctatcctct ggtttgattt ttggaatttg ttgttatgac
     2401 tcttcaatgc taattctctt gtaagctttt ttacacgcca taaacacgat tatgatgttt
     2461 tatattgtcg atatttcgtt gtccagactg gatatgtttg gaaatttgtt ttcatgcggg
     2521 ttagttcagc tggctttctg gatgagaaag tttgctgttt tgaccagttc gcgcttctga
     2581 aggggtgaaa ccgatcatta atcgcttttg tgcatagtta tgcaggcccc taaaaacgat
     2641 tctgacgcgt tttttgtgtt ttccctaggt ttatcttgtc tttttgagtt ttttgcgtca
     2701 gaaagcgatt gagagcgttt tagagggtac gtacaagagg agttatggta aatgggtctg
     2761 gttttcggga aggatcgaca ggatttgccg ttgggtgtag tgtaaccaac tgaaaaacaa
     2821 acgcccctga aattcgtgcc gatccgccaa gactgtcacg aaaattcaag gggcgtgtgg
     2881 gtcgtaacac acggaggaaa tcctaacaca tgagcgccgt acttcaactc ttcagggaaa
     2941 aattaccgca caaaccgtac tgtacgaacg atttcacgta cggcgttcgc attctaccga
     3001 aagatatcgc catccttgcc cgtttcatcc agcagaacca gccacatgcg cagcactggc
     3061 tggcctttga cgttgaccgg acgggggcag cgatcgactg gagcgaccgg aactgtccgg
     3121 ccccgaacat caccgtaaaa aatccacgta acgggcacgc gcatctgctc tacgcgctca
     3181 ctcttccggt gagaaccgcg ccggatgcat cggcttcggc gctcaaatac gctgccgtga
     3241 ttgagcgtgc gctgtgtgaa aaactgggcg cggatgtgaa ctacagcggc ctgatctgca
     3301 aaaatccgtt ccaccaggaa tggcaggtgg tggaatggcg ttgggaactc tataccctcg
     3361 acgaactggc ggattatctt gatttgagcg cctcagcgcg ccgtcgcgtc gataaagatt
     3421 acgggatggg gcgaaactgg tatctgttcg aaaagggccg taaatggtct tacagggcga
     3481 ttcgtcaggg ctggccagca ttctcaccgt ggcttgatgc agtgattcag cgtgtcgaaa
     3541 tgtacaacgc atcgcttccc gttccgcttt ctccggctga atgtcgggct attggcaaga
     3601 gtattgcgaa atacacctac cgcaaattct ctcctgaagg cttttccgcg gtacaggctg
     3661 ctcgaggtcg taagggcggt aatgcaaatt catcagaaaa tcaggctatt aaaggtcaga
     3721 aatcaaagcg tgtagccgtt ggcacatcgg cacgaactct gaagccgtgg gtgacgttag
     3781 ggatcagtcg tgccacatac tatcgaaaac taaaatgtga tccagatctc gcaaaatgag
     3841 accagataac aagccttatc agataacagc gcctgtaggc gtttttttga gcgggtaggt
     3901 ttggggtgat ttcccgtgtt tcgtttggca atggttttag cgtctgtgtg tgagtggtgg
     3961 ttgtgctcgc cgcagtctca atgaccgagc gtagcgagcg aatgagcgag gaagcaccag
     4021 ggaaccggaa cgtgaacgga ggctcttacg cactgtcttt ggtgagtagc tctttcccgc
     4081 gtttttccca ttcctgccat tttggatggt tgcgcggtag ctctgcgatt cctgcgagtg
     4141 cgcctaccag ttcggcagca ctaaactttg gttttccggt tttgctgtcc accagtcctg
     4201 ccacaatcat gaggcctgcg gccttgtaga gttcatgatc ccgcgccttt cgttccgccc
     4261 ttgcggctgc cttccgttct gccgctatta ttgccgttac cctggctttt gctgcggctg
     4321 ctttctctgc ggttttttct gcccgtatca gtgcggacaa cgttttttca tccgtcgttg
     4381 ttcggttttt tttctctgcc agtaacacaa gtaatctttg ctgctctgac ggtgatttca
     4441 gtccgttgat ataggcaatt tttgcactta accactcttc acgatttgtc attcttacct
     4501 ctgcactttt gccgttaatg tgagttgtta ttgtgcataa tatcaccttg tctgcctgcg
     4561 tgtgagacct taaaatcatc cctgattaat tcagggatgc gcacttagac gtttctctcc
     4621 ttcgtcgaga aacagtgcgc tcctgcggag ggcttaacgg cagatggcaa gctaccattg
     4681 tacagttaaa actggagcaa aaggcgtagc cttaaaacat gctgattata tttctagatc
     4741 cggcgaatat aagaactaca aatcgcggga ggatctggaa ttttcgtcat ccggtaacat
     4801 gccatcatgg gcgaagaaaa atcccgcaga gctatggaaa gcagcagatg aatttgaacg
     4861 aaaaaacggg acggcatacc gtgaaattga gatcgcatta ccgcgagaac tgacacgcga
     4921 acaacggata gaacttgttg aagatttcgt gcaaaaggag cttggtgatc gccatgccta
     4981 tcagtacgcg atccacaatc cgccaggtgc aatcgacgga aaggaacaac cacacgcaca
     5041 tatcatgttt tgcgagcgga ttaatgatgg tattgaacgc gatccgcagc agttttttaa
     5101 acgtgccaac agcaaatcac cggagcgggg aggtgcaaaa aaggcacgct ttggtgagac
     5161 accacaagag cgaaaatcag ccttggttgc gctacgttct cactgggctg atgtgcagaa
     5221 tgaacacctt gcgcggcacg gccatcagtc gcgcgttgat catcgttcac tgaaagaaca
     5281 gggtatcaag cgcacaccgg aagttcatct tggtcccgtt cgtgttgctg ttatgaatgc
     5341 tgatcaggtt tgtgcaattc tggcacggag aaacgcggaa cgggagaagc tagaagcaga
     5401 gcaggaacgg gacagcatca ttgaccttaa aacgaccttg aaggaagcgt tagctgaacg
     5461 ggataacata ccaccaagcc tggatgagct tggggcagaa ttgaaggcgt ttgttgaaag
     5521 ctcgtttgat gaactcaatg aggtaatgca gcttaattca ttgattaacg gtgcgctgga
     5581 ctcaatgatg aagcaattcc aggtggaaga ggagcggaag ttgcaacagg aacgactaat
     5641 tgaagccgaa aagcaaagag acctggagag ggaaagagaa agagtgcgcc agcgtgcgta
     5701 ttcctcacca gcacca
//
