LOCUS       NZ_CP145147             4087 bp    DNA     circular CON 05-APR-2024
DEFINITION  Escherichia coli strain CAVp367 plasmid pCAVP367-4087, complete
            sequence.
ACCESSION   NZ_CP145147
VERSION     NZ_CP145147.1
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 4087)
  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  JOURNAL   Unpublished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 4087)
  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
            CP145147.1.
            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..4087
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="CAVp367"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pCAVP367-4087"
                     /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            complement(join(3462..4087,1..82))
                     /locus_tag="LMH29_RS26655"
                     /old_locus_tag="LMH29_26655"
     CDS             complement(join(3462..4087,1..82))
                     /locus_tag="LMH29_RS26655"
                     /old_locus_tag="LMH29_26655"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001296720.1"
                     /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_001296720.1"
                     /translation="MTSNPLIAYKSNALVEASYKLTLQEQRFLLLCISRLNSGTDVASP
                     ELQKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRA
                     QYARGEGKAQITFSDAVMPYLTQLKGQFTRVVIKNISNLSRSYSIRIYEILQQFRSTGE
                     RIIALDDFKSSLMLDGKYKDFKTLNRDLIKPCVDELNKKSDLAVTVETIKKGRTVVALH
                     FRFKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(614..868)
                     /gene="mobC"
                     /locus_tag="LMH29_RS26660"
                     /old_locus_tag="LMH29_26660"
     CDS             complement(614..868)
                     /gene="mobC"
                     /locus_tag="LMH29_RS26660"
                     /old_locus_tag="LMH29_26660"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091745.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     gene            1047..3206
                     /gene="mobQ"
                     /locus_tag="LMH29_RS26665"
                     /old_locus_tag="LMH29_26665"
     CDS             1047..3206
                     /gene="mobQ"
                     /locus_tag="LMH29_RS26665"
                     /old_locus_tag="LMH29_26665"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_023142279.1"
                     /translation="MAIYHLSMKIISRNSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTEYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLATL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHATERRHDRGWSQ"
                     /name="mobQ"
     Typing          complement(870..1046)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          1047..1405
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(3463..4087)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          961..3203
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.599"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aacgctgttc ttgtaaagtt agcttgtaac tggcctcaac cagcgcattg gacttatagg
       61 ctatcagagg gtttgatgtc attttaacca ccaggccaaa aatgaggtga aataaaaacc
      121 tatcaccttt agcattggtg agcaattata ttttcacccc ccattttcct gtgaatatta
      181 ccttaaatct cctcaccttt accttaaatt acctcaccca agcaccttaa attatatcac
      241 ctttacctta aatcatatca cctatagcgt tgtaacattt tgttttctat aaggaatttt
      301 ggcgctaaaa caagtattaa aaacaagatc ttaaaaacaa gatctaaaaa cttaacgacg
      361 agcctgtgga taacttggag tgctgaaaac aaaaaaccaa taaaaacaat gcgttgcaaa
      421 aaagcagaat tgcaagttcc gaatacaccc cctccaaccc tgtggaaatc cagtattcat
      481 gcgggttcag cgcatatcac ctcccgaaaa accgtgcgta tgtgctcaat caggcgacgg
      541 attcacttcc gcttcctcgc ccactcgctc gctaacgctc ggtcgctggg actgcggcga
      601 gcggacgata caatcactgt cctggcagcg cttccagctc gttaatcagc ggcagtatgc
      661 gcgtcacatc agcctgtcgt gtcacctctg ccttcaggaa ctggagtaac caggcacgca
      721 actgcacctc ctccggcttt ctgacctttg ccagcaatgc tgcacccaca atgaccttct
      781 gcgctgtgtc cagactcctg ctcttcgcct tcaggcgctg taatctggcc tcagcatcag
      841 caatcttctg ttcgagtgtt ctgctcatga tgtaactccg tgcgcgatga aaaatcgcat
      901 tttagcgcgt cactggtagt ttaaaaactg agctggcata atgcacggaa aatcacgaag
      961 tgcgcactta tacaatctcc actccgtttc gattgtgtgc gccctgcggg gctgaaagaa
     1021 aaccacaaaa aggcattacg gcagaaatgg cgatttatca tctcagcatg aaaatcatct
     1081 ccagaaacag cggctacagc gccgttgctt ctgctgccta tcgttccggt tcactgatgc
     1141 ttgatgagcg taccggactg actcacgact acacccgcaa aagcggtgtg gctgaagctg
     1201 tgattctgac tcccgcgaca gcccctgcct ggtgtacgaa ccgtgccgaa ctctggaatg
     1261 ccgttgagaa ggccgaacgc cggaagaact cacaacttgc gcgggaaatt gaactcgcca
     1321 tcccccgcga actaccgcag gatgccgcac gggaaaccgt tctcgccttt gtcagagaaa
     1381 actttgtcag tcagggcatg attgctgatg tggcgttcca tcacatggat aaaacaaatc
     1441 cccatgcgca catcatgctg accacgagag ctgtcggacc tgctggattc ggtggaaagg
     1501 tcagggactg gaacgaccgg acacatgccg agacgtggcg tgcatcatgg gctgaccatg
     1561 cgaacagggc actggcgaac gccggttatc aggaagagat agaccatcgt tcatacgagc
     1621 gacaggggct tgagaaaacg cctggtattc acctcggaaa gtctgcctgt gcgatggaaa
     1681 cacgcggtat cgaaacagaa cgcggcgaac agaatcgtct gattaacaga cttaacctgg
     1741 aaatacagat ttcccgtacc gaactcagaa acagcgggct gacagagcct gcccgccgtg
     1801 tggctgacct tctgaatatc gtgcttcctg acaacgcaac ttcgtacaca ctacgtgaca
     1861 tcatcgaagc gttgccgaag gacagtaatg cggcatggaa actcaccagt aatgccatgt
     1921 cgatgatggc agatatgcag gcgacgcgca gacgctggga agagctgaac accgaacgaa
     1981 aggaagcgat gagccatgct gccagcctga aaaaatcatc gccgttttcg tccggttttt
     2041 cccgtattcc cctgatgcaa tgggcggcac cggaataccg tagcgaacag ggaaaaatcc
     2101 agtcgctgag ccagcaaatg gaaaaattgc gacagcatta ccggaaggtg gagaaacagg
     2161 acattcccgc gagtcagacg gcatttgaaa aacagtggca gcagtggggg gcatccggcc
     2221 ttgcagctct cagagtccag ttgcttaaac gtgaagagga attgcgccgg aaggagcagg
     2281 aggatacaga acgtagtcgc gcggagcgac gagcggaaca gctcaggaaa aatgacaatg
     2341 ccgttatgga ttcaggggta ctgagcgcag tcgttacgga gtatggcgag gcccccatgc
     2401 ctggtaacgg ggaaatgacc tgttaccttc tgcttcacaa ccggaacgga gaatacacgc
     2461 tctgggggaa cgagctggag aaataccgca ccagaatctt tgagcgtgtt gatttaatgc
     2521 gtgacaggag tggttatatc tgtgaccgaa gcgaaatcgg tcaacatcca ccactgcaac
     2581 gtgtttattc ctctgcgacc tttgagcaac ttctgacgca ggtttgccag acatggccgc
     2641 aatatacccg caatctccgc cagccgaaga catggccgga gtctttctgt cttggagaag
     2701 accgccagcc agccatgcca tcactggcag caaggaaggt ggattttacg cagggacgtc
     2761 tgctagcgac gctgatgccg gtaatgagtt ctgtcgaccg ggaaacccgc cagcttcagc
     2821 ttttgctggt catgggcgtg gatgactctc tgggcggtgt tgtccggctt aatggtacgc
     2881 tgtatcccgc gtttgccgtt ccctcagccg ataacagcca gctggtcatc agtgcactga
     2941 ccgataaggg gttacggtat gcagggtatg gtgttgccgt aaatcacgat gcagacagcc
     3001 acatatcacc tgcgccggaa cttatggagt ttcatctgaa aacccgtgag gcaccgcttt
     3061 ttgctgccgt caacacacca gaaaaacagc cggatcatct gttccgctcg ctgggtttta
     3121 atcgtacctg ggacgaatgg cggcgcgagg aagatgcacg aacacacgcc accgagagga
     3181 gacatgatcg cggttggtca cagtgaatgt gaacaatatt ttgttttgtt taacatcgtg
     3241 ttatgttcgt cgatgttctt cgatgttcat cgacagggat gaatgcaaga agcacacaca
     3301 taatgcaagc atagttttgt ttttccgccc ccgaaaaatg ggggttcttt tttcgctgca
     3361 ttagagcgct tttgacgcaa tttttcactt caatagtacc ttcgcactac taacacaaaa
     3421 aaaacgcagc agggagcgtt ttaggtgcct taaaatcgat tctagatcgt catcttgatc
     3481 tgtttgtctt ccttgaagcg aaaatgcagg gctacaaccg tgcgcccctt tttgatcgtc
     3541 tcaaccgtta cagccaggtc gctttttttg ttcagttcgt caacacaggg ttttattaga
     3601 tccctgttta acgttttgaa atctttatat ttaccatcaa gcatcagtga tgatttaaaa
     3661 tcatcgaggg cgataatacg ttccccagta ctgcggaatt gctggagaat ttcgtatatt
     3721 cttatgctgt aacttcttga taaattagaa atatttttaa tgacgactct ggtgaattgc
     3781 cccttcaact gtgtcagata aggcattacc gcgtcagaaa aagtgatttg tgctttcccc
     3841 tctcccctcg cgtactgtgc ccgatactga atccagcgga actcctcgcg cttctcgtcg
     3901 tccttgagaa tgatcgacct gtcccacaaa cgatcgatcg cttcctgtag ctgaacctcg
     3961 gcatttttcc gccccatatc agggaatgaa tcaaaatatt ccgcagctgt aatggtcatt
     4021 gtcttttgca attcaggtga agctacgtca gtaccggagt taagtcggct tatgcagagc
     4081 aataaga
//
