LOCUS       NZ_CP147581             5164 bp    DNA     circular CON 05-APR-2024
DEFINITION  Escherichia coli strain GN05476 plasmid unnamed5, complete sequence.
ACCESSION   NZ_CP147581
VERSION     NZ_CP147581.1
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 5164)
  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 5164)
  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
            CP147581.1.
            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..5164
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="GN05476"
                     /isolation_source="bloodstream"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="unnamed5"
                     /geo_loc_name="USA: Durham"
                     /lat_lon="36.0070 N 78.9371 W"
                     /collected_by="Duke Bloodstream Infection Biorepository"
     gene            1..222
                     /locus_tag="WCU38_RS25480"
                     /old_locus_tag="WCU38_25485"
     CDS             1..222
                     /locus_tag="WCU38_RS25480"
                     /old_locus_tag="WCU38_25485"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_019842149.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_019842149.1"
                     /translation="MAKLGENTPHIIDAAVDFMASSQAFREYLKKLPPDNTIPPDLTDE
                     HVPLYIRRLEYYRLLYRPKQTESYWKKR"
                     /name="hypothetical protein"
     gene            complement(276..809)
                     /locus_tag="WCU38_RS25485"
                     /old_locus_tag="WCU38_25490"
     CDS             complement(276..809)
                     /locus_tag="WCU38_RS25485"
                     /old_locus_tag="WCU38_25490"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221103.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000168767.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQKLDVAGLIGERISHDFQRLEESVANMKVNADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFCVLGWGMKTILDRNYNATAAVYQKVVTLED
                     KLAEKPVTGKSRKN"
                     /name="hypothetical protein"
     gene            complement(812..1738)
                     /locus_tag="WCU38_RS25490"
                     /old_locus_tag="WCU38_25495"
     CDS             complement(812..1738)
                     /locus_tag="WCU38_RS25490"
                     /old_locus_tag="WCU38_25495"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221102.1"
                     /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_019842150.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTPEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIDGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     LTQQKEQLRELRKRWEVKHNEHMRKHGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIREWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQDRTEPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            1915..2313
                     /locus_tag="WCU38_RS25495"
                     /old_locus_tag="WCU38_25500"
     CDS             1915..2313
                     /locus_tag="WCU38_RS25495"
                     /old_locus_tag="WCU38_25500"
                     /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_001222914.1"
                     /translation="MRISNIEWLKKRIGFIRKLGEQTARQRQIIDLIDNEAGLTEQERK
                     LLHVLATAEKNDLQAQESERKQAVQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELCYKKDRILQALKELKYDLETSPNPDA"
                     /name="hypothetical protein"
     gene            complement(2517..3431)
                     /locus_tag="WCU38_RS25500"
                     /old_locus_tag="WCU38_25505"
     CDS             complement(2517..3431)
                     /locus_tag="WCU38_RS25500"
                     /old_locus_tag="WCU38_25505"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001738986.1"
                     /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_019842151.1"
                     /translation="MSAALQYFDENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDRVGAAIDWSDRNSPAPNVTVKNPVNGHAHLLYALNIAVRTAPDSSVKA
                     LKYAAAIERSLCEKLDADANYSGLICKNPFHLEWQVKEWREEPYSLDELADYLDLSASA
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLEAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGSKSKRSTVATSARTL
                     KPWEALGISRAWYYQLKKRGLVE"
                     /name="replication initiation protein"
     Typing          complement(2518..3431)
                     /name="rep_cluster_2131"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.44"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(816..1738)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.701"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atggcaaaat taggtgaaaa caccccacat attatcgatg cagctgtaga ttttatggca
       61 tcaagccagg catttcgtga gtatctgaaa aaacttcccc ctgataacac aataccgcca
      121 gatcttactg atgagcacgt accgttatat atacgaaggc tggaatacta tcgactgctt
      181 tatcgaccaa agcagacaga atcatattgg aaaaaacggt gaacggttcg cgaaatcctt
      241 tcgcgctccg tgaggcgttg gacaaacgaa gcgcgtcagt ttttccggct cttacccgtg
      301 acaggtttct ccgccagttt atcttccagt gtcacaactt tctgatacac cgccgctgtg
      361 gcgttgtagt tcctgtcgag tattgttttc attccccatc cgagcacaca gaacataacc
      421 agaaaagcca ctgacacccc acccagccat ttccagctat accctttaag ggtgttgtat
      481 tcctgcacga tattgctgtg aattgtcgca atatccctgt tcagggcatc cgcgtttacc
      541 ttcatgtttg cgactgactc ttccagccgc tgaaaatcat ggctgatgcg ctcacctatc
      601 agccctgcta cgtccagctt ctgcacctcg tttctgactt catccctgac ctgttttgcc
      661 acaccgtcag aaatatcccg atatccgcga agtgtttccc ttgccacagc cagagaatca
      721 gcaacagctt tctgttgctc cattgcggta tgttgcagat gctccaccga taacaggagc
      781 gtgagtaatt tttcttctgt gctggccatg ttcagaatcc catagaaaat ccacgtgacg
      841 gtgatttaac ccgttcaggt tcagttcggt cctgtctgct cactctgtct ctcatgtcaa
      901 agccatgctc ccgcgcaaca tcatgttgaa gccttctgac cagttcatgt tgcttaaccg
      961 gagtgtccag ccattccctg atgtcatgcc cgaccgttcg cgcctgttca agatggcggg
     1021 aatagtccgg ttcagaccgt ttttgcatga tgtcatgacg ctgggcatca tcaagccgtc
     1081 cggcagcttc aaaacccaga tgcacttcgg gacgtcgttc aatgccctgt tctttcagcg
     1141 tccggcagtc aatgaagccc ctttcaaagc catgctttct catatgttcg ttgtgcttca
     1201 cctcccagcg ttttcgcaat tcccgcaact gctctttttg ctgagtgaga gtcaggcttc
     1261 cggaatcctt tttcgcacct ccccgctcgg gatacctggc gttatagcgc cggaaatact
     1321 gttccggtgt acgttcaatg ccatcattca cacgctgact catcatgata tgcgcatgag
     1381 gctgttcgcc gccgtcaatg ctcgctttcg gattgtgaat ggcaaaactc caggcgtgcc
     1441 gttcgccagc ttcctgacgt acaaaatcct gcaccagttc aaggcgctgt tccggtgtca
     1501 gttcacgggg taatgcaatt tcaagttccc tataggtcga accgttcgca cgttcaaact
     1561 ggtcagccgc ctgccagaaa tgggaaggat tatccctggc ccattccggc atgtttccgt
     1621 gtgcggaata ttccaaatcc tgacggtcgc ggtatttctc tttgcgctcg atgtaatcgg
     1681 cgtggtttgc agcctgcccc ttgccaccaa atttaacgct gaggtgatag gttgccacgg
     1741 tttcagccct ctgcaggagc gcactgtttc tcgacgaagg agagaaacat ataagtgcgc
     1801 ttccttctaa ttttacgaat tagcacggaa gataccccct gcacccgccg accgcaagcg
     1861 atatactgca cgaccacaac acaccgcaaa aaaacaccag ggagcatcac gaacatgcgc
     1921 atcagcaaca tcgaatggct gaagaaacgg atcggattca tcaggaagct cggagaacag
     1981 accgcacgac agagacagat tattgacctg atcgacaacg aagccggact cacagaacag
     2041 gaacgcaaac ttctccacgt actggcaaca gcggaaaaaa acgacttaca ggcacaggag
     2101 agcgaacgaa aacaggcggt ccaaaaacga atcgagggaa aaaaacaacg acgggaacgc
     2161 aatcaccggc tctttctcgc ggctgggcta ctgatcgaag caggactggt agacacaaaa
     2221 acaggcgagc tatgctataa aaaagacagg atattacagg cacttaagga acttaagtac
     2281 gatctggaga catccccaaa cccagacgcg taagtgcctc catccgtgtt ccgattccct
     2341 ggtgcttcct cgctcattcg ctcgctacgc tcggtcatga gactgcggcg agcactacca
     2401 ccacaatcac gcggaaagcc gcgccattgc agggctgaac ggggaaaaac ggcaaaaaac
     2461 ctgctgctca aaaagacgcc agaaaggcgc tgttatctga tataggctta tttggtctac
     2521 tctacgagac ctcgtttttt cagttggtaa taccaggcgc gactgatccc taatgcctcc
     2581 cacggtttca gcgtgcgtgc agatgtagct actgtgctgc gcttagactt agaaccgccc
     2641 ttgcgaccgc gtgcagcctg aatttctggc gtgtgcgtat cagccacata ctgtgcgaaa
     2701 gtttccggcg tgaagttcct gtgcgtgtat ttcgcaatgc tcttgccaat agcccgacat
     2761 tcagccagtg aaagcggaac gggaagcgat gcattgtaca tttcgacacg ctggatcacc
     2821 gcttcaagcc actgtgagaa cgctggccag ccctgacgaa tcgccctgta agcccatttg
     2881 cgcgtcattt cgaacagatg gcagtttctc cccattccgt aatgtttatc gatgctacgg
     2941 cgcgctgagg cgctcaaatc gagataatca gccagttcat cgagggagta gggttcctcg
     3001 cgccactcct tcacctgcca ttccaggtgg aacggatttt tgcaaatcag cccgctgtag
     3061 ttcgcgtctg cgtcaagttt ctcacacaac gagcgttcaa ttgcggcagc gtatttcagt
     3121 gccttaaccg aactgtccgg tgcggttctc acggcgatat tgagtgcgta aagcaggtgg
     3181 gcgtgcccgt tcacaggatt tttaacggtg acgttcggtg cgggtgagtt ccggtcgctc
     3241 cagtcgatcg ctgcccccac gcggtcaacg tcaaaaacca gccagaactg cgcatgaggc
     3301 tggttctgct ggatgtaccg agcaagaagc gcacgccctt tgccggagat gcgaagacca
     3361 aaagcgagat catccgtgtg atagggacgg tggggtaaat tttcgtcgaa gtattgaagc
     3421 gcggcgctca tgtgttacga ttccttccag gttatcgacc gacctcgccc ctgtattctc
     3481 gtgacaatct tggcggagag acacgaattt caggggcgtt tgtttttcag tcgcttacac
     3541 tacacccaac ggcaaatcct gtcgatcctt cccgaaaaac cgatccattt accataactc
     3601 ccgttgtacg taccctgtaa aacgccctca atcgctttct ggcgcaaaaa acgcaaaaag
     3661 acaagaaaac accaggccaa accagaaaaa cgcgtcagaa acgttttcag ggcgttgcat
     3721 aactatgcac gaaagcgatg tgcgatcggt ttcgtgcgtt ctgaacaccg aacggctcaa
     3781 aacgacaagt tttctcccct ggtgcgtggc gctctgacgg ggtttcctgt ttccaaactt
     3841 cacatctcgc caggacaaaa aaaaaccgac ctggggtcgg tggcaagaat cagagtctat
     3901 gggaaatatt ttagttatcg gatgctcaat attcacaaac gcaaaaaatg cctcagtgat
     3961 gccctaaaac aacctttcca gaaggagtcc gcgctttacg atgcacggaa gagataaaaa
     4021 accccacaaa agtggggaac caagagaaac aacaattaca ggttgttggt tgtgttcgaa
     4081 caacgatgaa gtagctacgc taaataataa ttaccgtaca ggccctacat attcaacact
     4141 aaatttaaga tcctgacgaa ggatttataa atgcacgaaa acacatagac agacaaattc
     4201 actaaattca tacacaaaaa caagtgtagt tttctaagta aattagattc gacaaccaat
     4261 tagtttatcc acatcgcatt ccactcttgc tacaccaatc acatttcttg atatgtaata
     4321 gcagaaaaaa taaaaccaga caccaataga ccaaaaaaca aacattcaac aagaaacatt
     4381 ttgaacaata tcacaaaact gtcacaacca tcatcagact attgaaaaaa actggttgct
     4441 gttttataaa agcgactgta acaacctcca ctctatagtt ccattagttt aaagtgtcac
     4501 acaaactgag catccatttg ttttccttac ttttgcccct gtattccaag gggttttttt
     4561 ataacttaaa gattagcaca ccacacaaaa acaataaaaa aaacgacaag ttatacaata
     4621 aaaccagtac tatccataca gctaattaca tataaatact attaaaccat ctggacatta
     4681 aaaataaact cttataacat aaaattaatg cggttccggt accatatgtc agggataatg
     4741 tgcaaatgga ggtatcggaa ctgcatttca gttcattatt aattaatgac aaaaaaaacc
     4801 tctgcgagcg cagagggggt aaggaatgtt cccggtcata atatgtcgat agtgtttata
     4861 tacatacaga acaagaacaa caaccagcca actaataaat attttatttt ttagagctga
     4921 aaccttaaag ctcacttcca ttccatacat tgttataaac cttatgttga aaactgaaag
     4981 taagtacggc agacttatta agttgcgtgc agtcttttca cgttatacaa acaagaacac
     5041 ctgcgaagtt atttctcctt acatatcccc ctatgccaac gggggatttt ttctggttca
     5101 ctaacgcata aataatagtg acaccctatc attcacaaac cgtgataata taaggattat
     5161 catc
//
