LOCUS       NZ_CP147582             5129 bp    DNA     circular CON 05-APR-2024
DEFINITION  Escherichia coli strain GN05476 plasmid unnamed6, complete sequence.
ACCESSION   NZ_CP147582
VERSION     NZ_CP147582.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN40123768
            Assembly: GCF_037273335.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5129)
  AUTHORS   Parsons,J.B., Sidders,A.E., Velez,A.Z., Hanson,B.M.,
            Angeles-Solano,M., Ruffin,F., Rowe,S.E., Arias,C.A., Fowler,V.G.
            Jr., Thaden,J.T. and Conlon,B.P.
  TITLE     In-patient evolution of a high-persister Escherichia coli strain
            with reduced in vivo antibiotic susceptibility
  JOURNAL   Proc Natl Acad Sci U S A 121 (3), e2314514121 (2024)
   PUBMED   38190524
REFERENCE   2  (bases 1 to 5129)
  AUTHORS   Hanson,B.M., Parsons,J.B. and Conlon,B.P.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-FEB-2024) Center for Antimicrobial Resistance and
            Microbial Genomics, The University of Texas Health Sciences Center,
            1200 Pressler St, Houston, TX 77030, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: NOV-2021
            Assembly Method                   :: Flye v. v2.8.3
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x
            Sequencing Technology :: Illumina NextSeq and Oxford Nanopore
            GridION X5
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_037273335.1-RS_2024_04_05
            Annotation Date                   :: 04/05/2024 19:14:17
            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)                     :: 5,293
            CDSs (total)                      :: 5,170
            Genes (coding)                    :: 4,941
            CDSs (with protein)               :: 4,941
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 95
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 229
            CDSs (without protein)            :: 229
            Pseudo Genes (ambiguous residues) :: 0 of 229
            Pseudo Genes (frameshifted)       :: 89 of 229
            Pseudo Genes (incomplete)         :: 146 of 229
            Pseudo Genes (internal stop)      :: 44 of 229
            Pseudo Genes (multiple problems)  :: 45 of 229
            Pseudo Genes (short protein)      :: 3 of 229
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP147582.1.
            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..5129
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="GN05476"
                     /isolation_source="bloodstream"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="unnamed6"
                     /geo_loc_name="USA: Durham"
                     /lat_lon="36.0070 N 78.9371 W"
                     /collected_by="Duke Bloodstream Infection Biorepository"
     gene            1..324
                     /locus_tag="WCU38_RS25505"
                     /old_locus_tag="WCU38_25510"
     CDS             1..324
                     /locus_tag="WCU38_RS25505"
                     /old_locus_tag="WCU38_25510"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001316561.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000533253.1"
                     /translation="MGRNMSAARTDGFIRNIHSRNPFDVIRADVVISRLEKQAHWGCGL
                     HYEIYEANLFDMAMNHLSRLPLKDRPVFIGAAARKGLFLTMEETRLAREAKDALMAELA
                     LEY"
                     /name="hypothetical protein"
     gene            383..625
                     /locus_tag="WCU38_RS25510"
                     /old_locus_tag="WCU38_25515"
     CDS             383..625
                     /locus_tag="WCU38_RS25510"
                     /old_locus_tag="WCU38_25515"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001398403.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000540588.1"
                     /translation="MGYITYVTDQRPGEPDILTGNTFADLEICDSDGHLLLKVSAPEAG
                     WTHESLNLVQPQEVQEGNDAFDAYLNGIWIGSTEV"
                     /name="hypothetical protein"
     gene            891..1175
                     /locus_tag="WCU38_RS25515"
                     /old_locus_tag="WCU38_25520"
     CDS             891..1175
                     /locus_tag="WCU38_RS25515"
                     /old_locus_tag="WCU38_25520"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001371319.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_072165043.1"
                     /translation="MSVTDDVVVPATATATATATATATATATATALLFPAALILTTAVL
                     SCLPGAPSAPGCLAASGRQARLRQAAAGAPASLRRTRWRGFGLSLRSDA"
                     /name="hypothetical protein"
     gene            1646..1942
                     /locus_tag="WCU38_RS25520"
                     /old_locus_tag="WCU38_25525"
     CDS             1646..1942
                     /locus_tag="WCU38_RS25520"
                     /old_locus_tag="WCU38_25525"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001545326.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001272251.1"
                     /translation="MSAFSFNTTYQPTGDQQKDAIAQIGIMQNRAVQANLAYQSCRDSG
                     ALFKVLHQVNNELHDLLDSLENHTPLVRKNADELIALLLLFTRQVGQSRTDLI"
                     /name="hypothetical protein"
     gene            2052..2870
                     /locus_tag="WCU38_RS25525"
                     /old_locus_tag="WCU38_25530"
                     /pseudo=""
     CDS             2052..2870
                     /locus_tag="WCU38_RS25525"
                     /old_locus_tag="WCU38_25530"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001234456.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="DUF932 domain-containing protein"
                     /name="DUF932 domain-containing protein"
     gene            complement(3171..3685)
                     /locus_tag="WCU38_RS25530"
                     /old_locus_tag="WCU38_25535"
                     /pseudo=""
     CDS             complement(3171..3685)
                     /locus_tag="WCU38_RS25530"
                     /old_locus_tag="WCU38_25535"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000759160.1"
                     /note="frameshifted; internal stop; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="transglycosylase SLT domain-containing protein"
                     /name="transglycosylase SLT domain-containing protein"
     gene            4102..4503
                     /gene="traM"
                     /locus_tag="WCU38_RS25535"
                     /old_locus_tag="WCU38_25540"
                     /pseudo=""
     CDS             4102..4503
                     /gene="traM"
                     /locus_tag="WCU38_RS25535"
                     /old_locus_tag="WCU38_25540"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001151523.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="conjugal transfer relaxosome DNA-binding protein
                     TraM"
                     /name="traM"
     gene            4603..4842
                     /locus_tag="WCU38_RS25540"
                     /old_locus_tag="WCU38_25545"
     CDS             4603..4842
                     /locus_tag="WCU38_RS25540"
                     /old_locus_tag="WCU38_25545"
                     /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="hypothetical protein"
                     /protein_id="WP_338838479.1"
                     /translation="MCAMDTRERALIRQSGLPEIILSAKYPVCVRTESGKFIDSNSVFL
                     HLIKCQNSDSEIWFSGIDIDTQILFHTAIMGCGG"
                     /name="hypothetical protein"
     Typing          3746..4022
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.429"
                     /coverage="100.0"
                     /evalue="1.1499999999999999e-126"
ORIGIN
        1 atgggcagaa atatgtcagc agcacgtacc gatggcttta ttcgtaatat tcattcccgc
       61 aatccctttg atgttatccg ggctgatgtg gtgatcagca ggctggaaaa gcaggctcat
      121 tggggatgtg gtctgcacta tgaaatttat gaagcgaatt tgtttgatat ggcgatgaat
      181 catctttccc ggcttcctct gaaggatcgt ccggtattca ttggtgctgc tgcacgaaag
      241 gggctttttc tgacgatgga agaaaccagg ctggcacggg aagcgaaaga tgctctgatg
      301 gctgaacttg ctctggaata ctgaaaatcg ggccgcaccg tcgtcccgga tagtgctgaa
      361 atatttaatg tggagagaat ggatgggata tatcacatat gttacagatc aacgacccgg
      421 tgaaccagat atcctgaccg ggaacacgtt tgctgatctg gagatttgtg attctgatgg
      481 gcatcttctg ctgaaagtgt ctgcacctga agccggctgg acacacgaaa gcctgaacct
      541 tgttcagccg caggaagtgc aggaggggaa tgatgcattt gatgcttatc tgaatggtat
      601 atggatcggt tcgacagagg tctgaacaaa tcacgccagc agaagacgtt gctggcgtct
      661 tctgcattcc cggggagctg tcgcacggca tgtttgctta tacccgtgcc ccgagatgat
      721 tatttgtctg cgggcctgaa gacgccgggc aggcgggagg ataaatgccc gtctgcccgc
      781 gccgggaaaa gacagcacgc cggtggcgct gaaagggggc gcgcttacgc tccgcccctt
      841 tcattacgcg gatgttctgc tgtgtgcttc tgtcttttca tgcctgtcat ttgtctgtta
      901 ctgatgatgt tgttgttcct gctactgcta ctgctactgc tactgctact gctactgcta
      961 ctgctactgc tactgctact gctcttcttt ttcctgccgc tctgattctg actactgcag
     1021 tgttgtcctg tctgccgggc gcaccttcgg ctcccggctg cctggcggca tccggtcgtc
     1081 aggcccgact ccgacaggca gctgctggcg cacccgccag tctccgccga acccgctggc
     1141 gcggtttcgg gctgtcgcta cggtccgatg cgtgaaaacc ccgggcttgc agcgaccgtt
     1201 ccggtcgcgc cgcctctgtc gcgccgtggc ctgcgctccc ggcatcccgg caaaaggccg
     1261 ccgggatgta aggcgcaacg ccgtttcgca aaccgcgctt cacgtcgttg cggcgggtcc
     1321 ctgcccgttg ttctgtccgg tgccattcac ctgtttaagc ccctgtcgcc gggggcatag
     1381 acagccacaa cctgccgcac tgactgtcca gggtaaatga acagcccaca aaatttttta
     1441 cccaaaaccc ggtaaaaaat tttgcgttct gcccaggaca ggtgcgtcag gccgtggcag
     1501 tgatgcccct tgcggcgaag gttctcaaac aggtgatggt gaataccgga gggaacaaaa
     1561 ggcaggtccc cgcaaaacgt caaaaccgcg gctcccgaaa ctcaacagat gatgggggct
     1621 gaaaacatca gatacaggag gaattatgag cgcattttct tttaacacca cttatcagcc
     1681 aacaggcgat cagcagaaag acgcaatcgc acaaatcggg atcatgcaga atcgtgctgt
     1741 tcaggcaaat cttgcatatc agagctgccg ggattctggt gcactcttta aggtgctcca
     1801 ccaggtcaat aatgagctgc atgacttact ggatagcctg gagaatcata ctcctcttgt
     1861 cagaaaaaac gctgatgagt tgatcgcgct gttactgctt ttcactcggc aggttggtca
     1921 gtcccgaact gacctgattt gatggtcctt cccctcggaa ttgttgtctt tttgttaacg
     1981 ataaccgagg gggatgatat taagcgaaaa aaattttatt aattttatgc cttcataaag
     2041 gagttactgt tatgcgatta gcttcccgtt ttggtcgata taattctatt cgccgtgagc
     2101 gcccgttaac ggatgacgaa ttaatgcagt ttgttccatc tgtcttttct ggtgataaac
     2161 atgaatcccg gagtgagcgt tatacatata tcccaaccat caatatcatc aataagttac
     2221 gtgatgaagg tttccagccg ttctttgcct gtcagagtcg ggttcgtgat ttgggacgcc
     2281 gcgaatacag taaacatatg ttacgtcttc gcagggaagg gcatattaac gggaaagaag
     2341 ttcctgaaat tatcctgctt aattcacatg atggttcatc cagttatcag atgatcccag
     2401 gaatttttcg ttttgtctgc acaaatggcc tggtgtgtgg gaataatttt ggcgaaatcc
     2461 gcgttccaca taaaggtgat attgtcgggc aggttattga gggagcgtat gaagtgctcg
     2521 gtgtctttga taaagtcact gaaaatatgg agacaatgaa agagatacat cttaacagtg
     2581 acgaacaaca tttatttggc agagctgcat tgataccagg tacgaagatg aaaataaaac
     2641 gccagtgacg ccagaacaaa taattactcc ccgccgttgg ggaggataaa cagaacgatc
     2701 tctggacaac ctggcagcgg gttcaggaga atatgataaa aggtggatta tcggggcgaa
     2761 gtgcctcggt aaataccaga acaagagcca ttacaggcat tgacggtgat atccgaatca
     2821 acaaagcatt atggatgatt gccgaacagt tcagggagtg gaagtcatga taatataagt
     2881 aaagccccga aaaatttttc ggggctttta cttatattat catcctgcaa cattgctgtg
     2941 tcgtctgata tgcctcaatt tcatcaactg gcttttcggt agtctgtaaa tattgtgccc
     3001 gcgaaaaatg gtctggcagg aggctgcgca gttactggat atatataaga tggggtctcg
     3061 ctttgcggga gcttcggtag aagtcagcat tatcactcat atgatatttt tgtgtgtggc
     3121 cttccatgcc gctgtcgcgg cataaccggt atttgacaat gtatacaata ttaattgttc
     3181 tgcacactgt taatttggga aagtgatttc ttcgtcggtc ggaacccgga tgccttttac
     3241 tgctctttat ccaggtataa atccggtaaa cctctctgat gcgtaagcaa gacgtctctg
     3301 gttctggcgt tcggtcttcc tgaatccggc attgtatgca ccaacggcct cccaggagac
     3361 gcccccattt ttttaaaggc tattgccaga taataagcac cggtataaat gttcatgcag
     3421 ggatctgttg tcagatgttc cagcgaattc catagcgggc cagttcgtta aaatgctggg
     3481 aatctacctg catcagtccg ctgccatatc ccgttaccgg attaataccg atggcattaa
     3541 cccggtaacg ggattctttc catgatattg ctctcagtaa atcaggatct attttgtaat
     3601 cccggcctgc aagatcaaag caatcagtgg catggcagat ctcatttata aacatctggc
     3661 agatggctaa catccatttt ttcatttttc cacctctggt gactttatcc gtaaataatt
     3721 taacccactc cacaaaaaag gctcaacagg ttggtggttc tcaccaccaa aagcaccaca
     3781 cactacgcaa aaacaagttt tttgctgatt tatctttaat acattgggtt gtatttgtgg
     3841 atttatattg tttaaatctg atttttttaa agcagcgtcg ttagctttaa tacagcaacg
     3901 cgccgacacc gctttgtagg ggtggtactg actattttta taaaaacatt attttatatt
     3961 aggggtgctg ctagcggcgc ggtgtgtttt tttataggat accgtcaggg gcgctgctag
     4021 cggtgcgtcc ctgtttgcgc tatgaattct agtgtttcga aatccaactt tgttttatgt
     4081 ttaaaaaaaa ggtaatatct aatggctaag gtgaatctgt atatcaacaa tgatgcttat
     4141 gaaaaaataa acgcgattat tgaaaaacgt cgacgggaag ggcgagagga aaagatgtca
     4201 gtttttcagc aacggcttca atgcttcttg aactgggtct tcgtgtatgt gagactcaga
     4261 tggagcgcaa agagtctgca tttaatcagg ccgagtttaa taaactactt cttgaatgcg
     4321 ttgtaaaaac acagtcatca gtagcgaaaa ttttgggtat tgagtctctc agtcctcatg
     4381 tctccaggaa atccaaagtt tgaatatgcc aatatggttg aagatatcag agagaaggtg
     4441 tcggctgaga tggaaaggtt ctttccaaaa aatgatgatg aattaaaggg aaataaattt
     4501 tgacttttgt tcaaatatca gactttttaa tggttcaaac tgatgacaat aatcagaata
     4561 attagtatat taattacgtg gtaatccttt gaggaggttc ctatgtgtgc gatggatact
     4621 agagaaagag cactcatacg tcaatcaggc ctgccggaaa ttattttatc cgcaaaatat
     4681 ccagtctgtg tccgcacaga gtcaggaaaa ttcatagact caaactctgt ttttttacac
     4741 ttaataaagt gtcagaatag tgattctgaa atatggtttt ctggtattga tattgatacg
     4801 caaattttat ttcatactgc tatcatggga tgtggtggtt gaaagtacgg aagtgaataa
     4861 cttgaatttg tttgtctgga gattctttga aagatacgta gttagtggct tttttataaa
     4921 gggcaaggag tttagttgtg aacctgacaa atatcgcttt aataagataa taccgtatct
     4981 tttgggttat agtcatgagt attcttctca gagaatggat atctctgttg accaatctaa
     5041 aaaaatattt atgaatttta aaaaacacta tggtttctca gaccgaaact caaaagatga
     5101 tgggggcaaa aaacagaggt gtattaaag
//
