LOCUS       CP137938                6200 bp    DNA     circular BCT 15-NOV-2023
DEFINITION  Escherichia coli strain 2023CK-00004 plasmid unnamed3, complete
            sequence.
ACCESSION   CP137938
VERSION     CP137938.1
DBLINK      BioProject: PRJNA288601
            BioSample: SAMN32801356
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6200)
  AUTHORS   Hergert,J., Casey,R., Wagner,J., Young,E.L. and Oakeson,K.F.
  TITLE     Pathogen: clinical or host-associated sample
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6200)
  CONSRTM   Clinical and Environmental Microbiology Branch: Whole genome
            sequencing antimicrobial resistance pathogens in the healthcare
            setting
  TITLE     Direct Submission
  JOURNAL   Submitted (19-JUN-2023) Division of Healthcare Quality Promotion, US
            Centers for Disease Control and Prevention, 1600 Clifton Rd,
            Atlanta, GA, USA
REFERENCE   3  (bases 1 to 6200)
  AUTHORS   Hergert,J., Casey,R., Wagner,J., Young,E.L. and Oakeson,K.F.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-NOV-2023) Utah Public Health Laboratory, Utah Public
            Health Laboratory Infectious Disease submission group, 4431 S 2700
            W, Salt Lake City, UT 84129, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.5.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 148.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 11/06/2023 11:42:27
            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)                     :: 4,892
            CDSs (total)                      :: 4,770
            Genes (coding)                    :: 4,492
            CDSs (with protein)               :: 4,492
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 278
            CDSs (without protein)            :: 278
            Pseudo Genes (ambiguous residues) :: 0 of 278
            Pseudo Genes (frameshifted)       :: 97 of 278
            Pseudo Genes (incomplete)         :: 193 of 278
            Pseudo Genes (internal stop)      :: 56 of 278
            Pseudo Genes (multiple problems)  :: 64 of 278
            Pseudo Genes (short protein)      :: 4 of 278
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            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/
FEATURES             Location/Qualifiers
     source          1..6200
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="2023CK-00004"
                     /isolation_source="other"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="unnamed3"
                     /geo_loc_name="USA"
                     /collection_date="2022-12-23"
     gene            join(6142..6200,1..91)
                     /locus_tag="PJR86_24425"
     CDS             join(6142..6200,1..91)
                     /locus_tag="PJR86_24425"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WPF10968.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGSPVG
                     REAL"
                     /name="hypothetical protein"
     gene            complement(836..1276)
                     /locus_tag="PJR86_24430"
     CDS             complement(836..1276)
                     /locus_tag="PJR86_24430"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011161230.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="entry exclusion protein 1"
                     /protein_id="WPF10969.1"
                     /translation="MAWHTVQETLKLTGKSRSQLYRDMAKGLVSYRTGKNDRREFETSE
                     LIRAYGELRTSETPKRHKEGHSKSVVSQAENAQLDVIQQKLDALQQTVTLMLEDKMARE
                     AENRLRNEEREQLQAEISRLADALAQEKKRGFWSRLFRSGSE"
                     /name="entry exclusion protein 1"
     gene            1494..1883
                     /locus_tag="PJR86_24435"
     CDS             1494..1883
                     /locus_tag="PJR86_24435"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000102614.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WPF10970.1"
                     /translation="MSTELNSGTVGGFGHMGPNDPYNDGHSGSGSSGGSFNGGGNGGHD
                     NSSGSSYTASFGLITGRHPITVPGTKNINSVDLSAVINNIIHHEGARNNMYLDTANNVR
                     VGVTGTGWQCLATAGISAEGKRTFR"
                     /name="hypothetical protein"
     gene            1927..2331
                     /locus_tag="PJR86_24440"
                     /pseudo=""
     CDS             1927..2331
                     /locus_tag="PJR86_24440"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001120888.1"
                     /note="incomplete; partial on complete genome; missing
                     C-terminus; Derived by automated computational analysis
                     using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS91 family transposase"
                     /name="IS91 family transposase"
     gene            complement(2438..3274)
                     /locus_tag="PJR86_24445"
     CDS             complement(2438..3274)
                     /locus_tag="PJR86_24445"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000480972.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="aminoglycoside O-phosphotransferase APH(6)-Id"
                     /protein_id="WPF10971.1"
                     /translation="MFMPPVFPAHWHVSQPVLIADTFSSLVWKVSLPDGTPAIVKGLKP
                     IEDIADELRGADYLVWRNGRGAVRLLGRENNLMLLEYAGERMLSHIVAEHGDYQATEIA
                     AELMAKLYAASEEPLPSALLPIRDRFAALFQRARDDQNAGCQTDYVHAAIIADQMMSNA
                     SELRGLHGDLHHENIMFSSRGWLVIDPVGLVGEVGFGAANMFYDPADRDDLCLDPRRIA
                     QMADAFSRALDVDPRRLLDQAYAYGCLSAAWNADGEEEQRDLAIAAAIKQVRQTSY"
                     /name="aminoglycoside O-phosphotransferase APH(6)-Id"
     gene            complement(3274..4077)
                     /gene="aph(3'')-Ib"
                     /locus_tag="PJR86_24450"
     ARG             complement(3278..4077)
                     /name="aph(3'')-Ib"
                     /gene="aph(3'')-Ib"
                     /gene_name="aminoglycoside O-phosphotransferase
                     APH(3'')-Ib"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            complement(4138..4953)
                     /gene="sul2"
                     /locus_tag="PJR86_24455"
     ARG             complement(4142..4953)
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            complement(5413..5571)
                     /locus_tag="PJR86_24460"
     CDS             complement(5413..5571)
                     /locus_tag="PJR86_24460"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WPF10967.1"
                     /translation="MHEPPVQSDRCALSGNYQLESNPERHDKTPLAAAISNRSAREDRL
                     RGLEVEA"
                     /name="replication initiation protein"
     ARG             complement(2442..3274)
                     /name="aph(6)-Id"
                     /gene="aph(6)-Id"
                     /gene_name="aminoglycoside O-phosphotransferase APH(6)-Id"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          5934..6107
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          complement(5405..6010)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.593"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 tgaccttttt gatttaatgg cgcaggttac tgaagagaac ctgcatgccc ctgtggattt
       61 tgggtcgcct gtcggccggg aagcgttata gctttttcgc ttgcccgcgt acgtggtaat
      121 actccggtat taccttttat ttctttattt tcatgtaatt acagtggatt tttaataccc
      181 gggtattact cgtgaaaacg aaatattcct tttttttctt ttaattcatg cagttgcgat
      241 gaaaatcgcg gctgcgttag gtgtatgacc attttgaggt tgaaaaataa tcaaccatgg
      301 cgggtgattt acgcaggtta aggggagatc gtgacaaaaa aagcgttcct cactgtatcg
      361 ttcatgcctg catgaacggg ttattcttcc tgactacaga attacatcgc tccttcagtt
      421 catacatcac ttttacatca cttatacatc acttttacat cattccttca gctcatacgt
      481 cactttcatc ctctgtgcca tttgtacatc acccccttcc tgaacgtgct gacagcgggt
      541 tttccggctg cgccggcaac gcttcacggc cacgcaataa attgcgtccc cgttcaccgt
      601 tttcggatgg gaagaacgcc ggaaacagga cttaccccgg ctgaatggtg tgaatttccg
      661 cgctatgcac ttgtgcgcat actcatgcat gccgtaaaaa cagagcctgc gcgtttctgg
      721 cgggttttcg ggtggtttgt tgcctgtttt accggtttcc cgtcagaaac gccctgaggg
      781 cctctcaggc ggtgctgata acagatgtta tggtaaatca gagtcacctg cactgttact
      841 ctgaaccgga gcgaaacagc cgcgaccaga atccccgctt tttttcctgt gccagcgcgt
      901 cagccagacg gctaatttcg gcctgtagtt gttccctctc ctcatttcgc aggcggtttt
      961 ctgcttcccg cgccatcttg tcttcaagca ttagggtaac agtctgctgc agagcgtcca
     1021 gtttctgctg aatgacgtct agctgagcat tttccgcctg gctaacgaca gatttggagt
     1081 gtccctcctt gtgccttttt ggtgtctcag aagtgcgcag ctcgccatag gcccgaatca
     1141 gttcactggt ctcgaactcc cggcgatcat tttttcctgt gcgatagctg acaaggcctt
     1201 tagccatgtc acgatataat tgcgagcgcg actttcctgt taatttcagt gtctcttgaa
     1261 ctgtgtgcca tgccataaaa gtgacagtgt ctcctgtgtg taccgtattg taacagcaga
     1321 acatattact gttttaacac aaaaggtctg aggctgcccg tgaggcgtga aaaatacaca
     1381 aaaaacctgt tgacggtgtg gttttgacgg gcgtagtatt tcgaatactg tatataaaca
     1441 cattgttata aatacagttt ttgctgtttt taaaagtcaa agaggataat tttatgagta
     1501 cagagttaaa tagcggtact gtcggtggtt ttggtcacat gggaccaaat gacccctaca
     1561 atgatggtca tagcggctct ggaagttcgg gaggtagttt taacggtggt ggtaatggtg
     1621 gccatgataa tagtagtggt tcatcttata ctgcatcctt tggtctcatc actggccgac
     1681 acccgataac tgtcccaggt acgaagaata ttaattctgt cgatctttct gctgtcatta
     1741 ataacattat acatcatgaa ggtgcacgca ataacatgta cctagatact gcgaacaatg
     1801 taagagtggg agtgacgggc actggctggc aatgtctagc aacggcaggc atttcggctg
     1861 agggtaaaag aactttccgc taagcgatag actgtatgta aacacagtat tgcaaggacg
     1921 cggaacatgc ctcatgtggc ggccaggacg gccagccggg atcgggatac tggtcgttac
     1981 cagagccacc gacccgagca aacccttctc tatcagatcg ttgacgagta ttacccggca
     2041 ttcgctgcgc ttatggcaga gcagggaaag gaattgccgg gctatgtgca acgggaattt
     2101 gaagaatttc tccaatgcgg gcggctggag catggctttc tacgggttcg ctgcgagtct
     2161 tgccacgccg agcacctggt cgctttcagc tgtaagcgtc gcggtttctg cccgagctgt
     2221 ggggcgcggc ggatggccga aagtgccgcc ttgctggttg atgaagtact gcctgaacaa
     2281 cccatgcgtc agtgggtgtt gagcttcccg tttcagctgc gtttcctgtt tggggtcgtt
     2341 tgcgggaagg ggcggaatcc tacgctaagg ctttggccag cgatattctc cggtgagatt
     2401 gatgtgttcc caggggatag gagaagtcgc ttgatatcta gtatgacgtc tgtcgcacct
     2461 gcttgatcgc ggccgcgata gctagatcgc gttgctcctc ttctccatcc gcgttccaag
     2521 ctgcggaaag gcacccataa gcgtacgcct ggtcgagcag gcgacgcgga tcgacgtcca
     2581 gcgcacgaga gaatgcgtcc gccatctgtg caatgcgtct aggatcgaga caaaggtcgt
     2641 ctctgtcagc cggatcgtag aacatattgg cggcgccaaa gcccacttca ccgaccagac
     2701 cgacgggatc tatcaccagc cagccgcgac tggagaacat gatgttttca tgatgcagat
     2761 cgccatgtag cccacgcagt tccgaggcat tgctcatcat ttgatcggct ataatcgccg
     2821 cgtggacgta gtcagtttga caacctgcgt tttgatcatc gcgcgcccgc tgaaacaaag
     2881 ctgcaaagcg atcccggatc gggagaaggg cagaaggcag gggttcctca gatgcggcat
     2941 acagcttcgc cattagttcc gctgcaattt cggtcgcctg gtagtcgccg tgctcggcaa
     3001 cgatgtgaga gagcattcgc tccccggcat attcgagcaa catcagattg ttctcacgac
     3061 cgagcaaccg gactgctccc ctcccattgc gccataccag atagtcggcc ccgcgcagtt
     3121 catcagcaat gtcttctata ggtttcaatc ccttgacgat tgcaggagtc ccgtctggca
     3181 atgaaacttt ccaaacgagg ctggaaaagg tgtccgcaat gagaacaggt tgcgaaacgt
     3241 gccaatgagc aggaaaaaca ggcggcatga acatcaaccc caagtcagag ggtccaatcg
     3301 cagatagaag gcaaggcgtt cgcggtcggg ggcttcgatc cccaatacat tgaataggac
     3361 agcgaaggcg cgctctgctt catctggcgc tgcccagttc tcttcggcgt tagcaatcat
     3421 gagtgccaaa tcggcatagc gatctgctgt tccgagccgc ccaaggtcga tcagacccgt
     3481 gcattgaaga gttttagggt ccaccatgaa gttcggcatg cagggatcac catggcaaac
     3541 aaccatatcg gtgcgctctt ggtcgagccg caccggtagc tctcgttcga cacgagccaa
     3601 aagatcgagc tgcggcgtac tcttgtcctc gtccggtaag aagtcgggat tgacggcatt
     3661 gcgggacacc acatcaacgg cgcgtccgaa cattcgcgac agcctgcgct caaacggaca
     3721 ttgatcaacc gataggctgt gaacagcgcc aagttgctgc cccattgacg gccacgcttt
     3781 gagcaaatcc gctccagaca gatcagccgc cggtactccc ggaattgccg ttatcaccaa
     3841 gcatgcaccc tcctgttcct cctgccagtt gatgacctcg gggcaagcca cacctcgacc
     3901 tttgagccaa atgaggcggt cacgctctcc agcgagctca ccgcggcggg aagcaggtgc
     3961 gattttcgcg aaggcatgcc cgtcaccacg tcgaaaaaca aaatcaccag attctccgcc
     4021 tctgacaggc aaccagtcag aatgcgattc accaaaaaaa atattagttc gattcaatgg
     4081 aggttccttc agttttctga tgaagcgcga atatagagaa atatcccgaa tgtgcagtta
     4141 acgaattctt gcggtttctt tcagcgccgc caataccgcc agcccgtcgc gcaaggggcg
     4201 cggctcgtgt gtgcggatga agtcagctcc acctgcggcg gcggcaagct ctgcagcgag
     4261 tgtcgcggcc ccgacatccc ccggaccacg gcctgtgagc gcgcgcagaa aggatttgcg
     4321 cgaaacagac agaagcaccg gcaaatcgaa gcgcagccgc aattcatcga accgcgccag
     4381 caccgagagc gaggtttcgg gagcagcccc cagaaaaaac cccatgccgg gatcaaggac
     4441 aaggcggttg cgtttgatac cggcacccgt cagcgccgcg atgcgcgcgt caaagaacgc
     4501 cgcaatgtga tccatgatgt cgccagcggg tgcctcgcgc cgatctgcct gcccgtcttg
     4561 caccgaatgc ataacgacga gtttggcaga tgatttcgcc aattgcggat agaacgcagc
     4621 gtctggaaaa ccgcgaatat cattgagata ggccacacca cgcgacaagg cataggcttg
     4681 cgtcgcgggt tgataactgt cgagcgagac gggaatgcca tctgccttga gcgcgtccag
     4741 caccggcgcg atacgcgcga tttctgtgtc ggacgaaaca ggcgcggcgt cgggattgct
     4801 ggatgccgga ccgaggtcga tcacatctgc cccctcggcc atcagcttac gcgcctgcgc
     4861 aatggctgcg tctggcgcca gataccggcc tccatcggag aaactgtccg aggttatgtt
     4921 gacgatgccg aaaatgatga gcgatttatt catgggggct tctataataa taataatcga
     4981 gcatgagtct catacggatg ctcgggtcga aagggaatcc ccaggcgagt aacctgtttg
     5041 cggtgatccg tttcatgatg atgtatctgt agcattttgg aaataaatat atcatctctc
     5101 aataagtaga tatatttatc ttttttgctt ctttggtgct gcaagtcacc aatacgaggg
     5161 aaacctgtta cggagcggtt taaccgtaat caacagtgac tggtgtcatg ttcggaagat
     5221 taattgatag taatctacaa aggatcttct tgagatcctt ttcaatgaat cgtaatctct
     5281 tgctctgtaa acgaaaaaac cgcctgggga ggcggtttgt tcgaaggtta agtcagttgg
     5341 ggaactgctt aacccggtaa cagggttcac gagaccgcca ttaccaaaac tgttctttca
     5401 gtgtagccgc agtcaggcct ctacttcaag acctcttaat ctatcttctc gtgcactcct
     5461 gttactaatg gctgctgcca gtggcgtttt gtcgtgtctt tccgggttgg actcaagttg
     5521 atagttaccg gacaaggcgc agcggtcgga ctgaacgggg ggttcgtgca tacagtccag
     5581 cttggagcga actgccttca cggaactgag tgtcaggcgt ggaatgagaa accgcggcca
     5641 taacagcgga atgacaccgg taaaccgaaa ggcaggaaca ggagagcgca cgagggagct
     5701 accaggggga aacgcctggg atctttatag tcctgtcggg tttcgccacc actgatttga
     5761 gcgtcagatt ttgcgatgct tgtcaggggg gcggagccta tggaaaaacg gcttcgccgt
     5821 ggccttatct cttctttgct aagtgtcttc ctggtatctt ccaggaaatt tccgtccccg
     5881 tccgtaagcc ggtaccgctc gccgcagccg aacgaccgag cgtagcgagt cagtgagcga
     5941 ggaagcggaa tatctcctgt atcgcatatt ctgctgacgc gccggtgctg ccttttttct
     6001 cctgccacat gaagcacttc actgattttc gcaatcgtgg caacatagta agccagtata
     6061 cactccgcta gcgctacatg actggttcag ggctgcgccc cgaaacccgc taacaacctc
     6121 tcagctactg gatatcaccc catgccatct gaatatgatg aacaactgga ttcgactgat
     6181 acgcagcttc ccggcgaata
//
