LOCUS       NZ_CP116487             4091 bp    DNA     circular CON 27-FEB-2024
DEFINITION  Escherichia coli strain GTEN_24 plasmid unnamed7, complete sequence.
ACCESSION   NZ_CP116487
VERSION     NZ_CP116487.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11230615
            Assembly: GCF_028215995.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4091)
  AUTHORS   Yorki,S., Shea,T., Worby,C.J., Cuomo,C., LaRocque,R.C., Manson,A.L.
            and Earl,A.M.
  TITLE     Comparison of long and short read metagenomic assembly for
            low-abundance species and resistance genes
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4091)
  AUTHORS   Yorki,S., LaRocque,R.C., Worby,C.J., Shea,T., Earl,A.M.,
            Walker,B.J., Manson,A.L., Sridhar,S., Turbett,S., Becker,M.,
            Oliver,E., Bronson,R., Leung,D., Knouse,M., Hagmann,S., Kelly,P.,
            Harris,J. and Ryan,E.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-JAN-2023) Infectious Diseases & Microbiome, Broad
            Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/27/2024 02:21:11
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,977
            CDSs (total)                      :: 4,853
            Genes (coding)                    :: 4,676
            CDSs (with protein)               :: 4,676
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 177
            CDSs (without protein)            :: 177
            Pseudo Genes (ambiguous residues) :: 0 of 177
            Pseudo Genes (frameshifted)       :: 69 of 177
            Pseudo Genes (incomplete)         :: 118 of 177
            Pseudo Genes (internal stop)      :: 28 of 177
            Pseudo Genes (multiple problems)  :: 33 of 177
            Pseudo Genes (short protein)      :: 2 of 177
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP116487.1.
            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..4091
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="GTEN_24"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="unnamed7"
                     /geo_loc_name="USA: Massachusetts"
                     /collection_date="2018"
                     /collected_by="Massachusetts General Hospital"
     gene            complement(join(3848..4091,1..1904))
                     /gene="mobQ"
                     /locus_tag="E5Q65_RS24820"
     CDS             complement(join(3848..4091,1..1904))
                     /gene="mobQ"
                     /locus_tag="E5Q65_RS24820"
                     /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_024236174.1"
                     /translation="MAIYHLSMKILSRSKGYSAVASAAYRAGEKILDERTGVIHDYTRK
                     NGVASAVILTPANAPAWCANRAELWNAVEKAERRKNSQLAREFELAIPRELAQDAARET
                     VLNFVRENFVSRGMIADVAFHNLGGSNPHAHIMLSMRAITPDGFGEKVREWNDWTHAET
                     WRGSWADHANRALANAGYQEEIDHRSYERQGVEKTPGIHLGKSACAMEKWGIETERGEQ
                     NRLINRLNLEIQVSRDELRNSELTEPARRMADLLNIELPDNATSYILHDIIEALPTDSN
                     AAWKLTSKAMSMMADMQATRRRWEDLNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWV
                     APEYGREQEKIQSLSQRMEKLRQHHWKVEKQDIPASQKAFETQWQQWGASGLADLREQL
                     RKREEELRRKEQEETERRRAEQLRRNDNAVMDSGVLKAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRARIFESVDLMRDRSGYICERSEIGQRPPLQHVYSSATFEQ
                     LLTQVCQTWPQHTRDLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSMGGVVRLNGTLYPAFAVPTADNSQLVINALTDKGLRFA
                     GYGEAVNHDADSPARPAPELMQFHLKTWSEPLFAIVNTPEKQPDHLFRSLGFERTWDEW
                     QRDEYARTHATERRHDRGWSQ"
                     /name="mobQ"
     gene            2075..2365
                     /locus_tag="E5Q65_RS24825"
     CDS             2075..2365
                     /locus_tag="E5Q65_RS24825"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001514113.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="mobilization protein"
                     /protein_id="WP_221925645.1"
                     /translation="MSRALEQKIADAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     GETQLRAWLLHLLKTEVTRQADVSRIQPLIDELNALPKPVPKEVSENDQQA"
                     /name="mobilization protein"
     gene            2898..3599
                     /locus_tag="E5Q65_RS24830"
     CDS             2898..3599
                     /locus_tag="E5Q65_RS24830"
                     /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_011666799.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCIGRLKSGSDAESTEL
                     QKTMTVTAEEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRAQY
                     AKGEGKAQITFSDAVMPYLTQLKGQFTRVVIKNISNLSRSYSIRIYELLQQFRSTGERI
                     IALDDFRSMLDIEHKYQTYKSLNQQLLRPCVDELNQKSDLAVTLETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     Typing          1550..1904
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1921..2071
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.81"
                     /coverage="85.0"
                     /evalue="3.53e-55"
     Typing          2899..3598
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.301"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(4..1946)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.846"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gcaaagcgta aacctttgtc ggtcagtgca ttgattacca gctggctgtt gtcggctgtg
       61 gggacggcaa acgcgggata cagcgtacca ttaagccgga caacaccgcc catagagtca
      121 tccacaccca tgaccagcaa aagctgaagc tggcgggttt cacggtcgac agaactcatt
      181 accggcatca gagtcggtgg cagacgtccc tgcgtaaaat ccaccttcct tgccgccagt
      241 gatggcatgg ctggctggcg gtcttctcca agacagaaag actccggcca tgtcttcggc
      301 tggcggagat cgcgggtatg ttgcggccat gtctggcaaa cctgcgtcag cagttgctca
      361 aaggtcgcag aggaataaac atgttgcagt ggtggacgtt gaccgatttc gcttcgctca
      421 cagatataac cactcctgtc acgcattaaa tcaacactct caaaaattct ggcgcggtat
      481 ttctccagtt cgttccccca gagcgtatat tctccgttcc ggttgtgaag cagaaggtaa
      541 caggtcattt ccccgttacc tggcatgggg gcctcgccat accccgtaac gactgctttc
      601 agtacccctg aatccataac ggcattgtca tttctcctga gctgctccgc ccgacgacgt
      661 tctgtttcct cctgctcctt ccggcgcaat tcctcttcac gtttacgcaa ctgttctcgg
      721 agatctgcaa ggccagatgc accccactgc tgccactgtg tttcaaatgc tttttgactc
      781 gcgggaatgt cctgtttctc aaccttccag tgatgctgcc gcaatttttc catgcgctgg
      841 ctcaacgact ggattttttc ctgttcgcgg ccgtattccg gtgcaaccca ttgcatcagg
      901 ggaatacggg aaaaaccgga cgaaaacggc gatgattttt tcaggctggc agcatggctc
      961 atcgcttcct ttcgttcggt gttcagatct tcccagcgtc tgcgcgtcgc ctgcatatct
     1021 gccatcatcg acatggcttt actggtgagt ttccatgctg cgttactgtc cgtcggcaac
     1081 gcttcgatga tgtcatgcag tatgtacgaa gttgcgttgt caggaagctc aatattcaga
     1141 aggtcagcca tacggcgtgc gggctctgtc agctcactgt tcctgagttc gtcgcgggaa
     1201 acctgtattt ccaggttaag cctgttaatc aggcgattct gttcgccgcg ttctgtttcg
     1261 atgccccact tttccatcgc acaggccgac tttccgaggt gaatgccagg cgttttctca
     1321 accccctgtc gctcgtatga acgatggtct atctcttcct gataaccggc gttcgccagc
     1381 gccctgttcg catggtctgc ccatgatccc cgccatgttt cggcgtgagt ccagtcattc
     1441 cactcacgga ctttctcccc gaagccgtca ggcgtgattg ccctcatgga tagcatgatg
     1501 tgcgcgtgtg ggtttgaccc gcccagattg tgaaaggcca cgtcggcgat catgccgcga
     1561 ctgacaaagt tttcccttac gaagttgaga actgtttccc gtgcggcatc ctgcgccagt
     1621 tcacggggga tggcgagttc gaactcccgc gcaagttgtg agtttttccg ccgctcggct
     1681 ttttcaacag cattccagag ttcggcgcgg ttcgcacacc atgctggggc gtttgctggc
     1741 gtcagaatca ctgcgctggc tacaccgttt ttgcgggtgt agtcgtgaat cactccggtg
     1801 cgctcatcca gtattttttc tccggcacga taggcagcag aagcaacggc gctgtagccc
     1861 ttgcttctgg aaagaatctt catgctgaga tgataaattg ccatcgtgtc gttgttgccg
     1921 ttttctttta gccccgcagg gcgcacacaa actcgacgaa ggagagtttg tataagtgcg
     1981 cacttcgtga tttgctgtgc attatgccag ttcagttttt aaactaccag tgacgcgcta
     2041 aaatgcgatt tttcaccgcg cacggagtta cggaatgagt agagcactcg aacagaagat
     2101 tgccgatgct gaggccagat tgcagcgtct gaaggcgaag agcaggagcc tggacacagc
     2161 gcagaaggtc attgtgggag cggcattgct ggcaaaggtc aggaagcctg gggaaacaca
     2221 actacgagcc tggttgcttc atctcctgaa gacagaggta acacggcagg ctgatgtgag
     2281 caggatacag ccgttgattg acgaactgaa cgcgttacca aaaccagtcc ccaaagaagt
     2341 gtcagaaaac gaccaacagg cgtgaatgca ccgtccgctc gccgcagccc cagcgaccga
     2401 gcgttagcga gcgagtgggc gaggaagcgg aagtgaatcc gtcgccagat tgagcacata
     2461 cgcacggttt ttcgacaggt gatatgcgct gaacccgcat gaatactgga tttccacagg
     2521 gttgagcggg gttttgttaa agcttgcgaa cctgcttttt tgtaacctgt tgtttttcat
     2581 gattttttgt tttgaacacc ccaagttttc cacaggctcg ccgttaagtt tttagatctt
     2641 gtttttaaga tcttgttttt aatacttgtt ttagggtcga attttcttat gaaattcaag
     2701 agtttagaag actataggta atataattta aggtaaaggc aatatgattt aaggtggata
     2761 ggcaatatga tttaaggtaa aggcaatatg atttaaggta atattcacag gaaaagggat
     2821 attaaaatta aatcatattg cctttaccta aaggaatgtt tatattttac tcattacctt
     2881 aggttgaggg atttacaatg tcggatctga ttgcctacaa atccaatgca ctggttgagg
     2941 ccagctataa attgactctt caggaacagc gattcttgtt actttgcatt ggtcgattga
     3001 agtcgggttc tgatgcagaa tccactgaat tgcaaaagac catgactgtt accgccgaag
     3061 agtatttcga ctcattccct gatatggggc ggaaaaatgc cgaggttcag ctacaggaag
     3121 caattgatcg tttgtgggac aggtcgatca tccttaagga cgatgagaag cgcgaggagt
     3181 tccgctggat ccagtatcgg gcacagtacg ctaaaggtga gggcaaagcc caaatcactt
     3241 tttcagatgc ggtcatgcct tatctgacac agttgaaggg gcaatttact agagttgtaa
     3301 ttaagaacat ctccaattta tcaagaagtt acagcataag aatatacgaa cttctccagc
     3361 aattccgcag cacaggggaa cgtattatcg ccctcgatga ttttcgctca atgcttgata
     3421 tagagcataa atatcaaaca tataagtctc tgaaccagca attattaaga ccttgcgttg
     3481 acgaactgaa tcaaaaaagc gacttggctg taacgcttga gacgatcaag aaggggcgca
     3541 cggttgtagc cctgcatttt cgcttcaagg aagacaaaca gatcaagatg acgatctaga
     3601 atcgatttta aggcctctaa aacgctctct gacgcgtttt ttttgtgttt ggcatgcgaa
     3661 ggtactggtg aagtaaaaaa ttgcgtcata aacgctctgg cacagtgaaa aaagaacccc
     3721 caatttttcg ggggcgggaa aactataaag ttgatttgtg ttatgtgtgt gcttcttgca
     3781 ttcatccctg tcgatgaaca tcgacgaaca taacacgatg ttaaacaaaa caaaatattg
     3841 gtcacattca ctgtgaccaa ccgcgatcat gtctcctctc ggtggcgtgt gttcgggcat
     3901 attcatcacg ttgccattca tcccaggtgc gctcaaagcc cagcgagcgg aacagatgat
     3961 ccggctgttt ttctggcgtg ttgacgatag caaaaagcgg ttcgctccag gttttcagat
     4021 gaaactgcat aagttccggc gcaggacgtg ccggactgtc agcatcgtgg tttaccgctt
     4081 caccatagcc t
//
