LOCUS       NZ_CP147556             5403 bp    DNA     circular CON 05-APR-2024
DEFINITION  Escherichia coli strain GN05064 plasmid unnamed2, complete sequence.
ACCESSION   NZ_CP147556
VERSION     NZ_CP147556.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN40123757
            Assembly: GCF_037287475.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5403)
  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 5403)
  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_037287475.1-RS_2024_04_05
            Annotation Date                   :: 04/05/2024 19:12:49
            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)                     :: 5,277
            CDSs (total)                      :: 5,160
            Genes (coding)                    :: 4,936
            CDSs (with protein)               :: 4,936
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 224
            CDSs (without protein)            :: 224
            Pseudo Genes (ambiguous residues) :: 0 of 224
            Pseudo Genes (frameshifted)       :: 89 of 224
            Pseudo Genes (incomplete)         :: 158 of 224
            Pseudo Genes (internal stop)      :: 43 of 224
            Pseudo Genes (multiple problems)  :: 59 of 224
            Pseudo Genes (short protein)      :: 4 of 224
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP147556.1.
            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..5403
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="GN05064"
                     /isolation_source="bloodstream"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="unnamed2"
                     /geo_loc_name="USA: Durham"
                     /lat_lon="36.0070 N 78.9371 W"
                     /collected_by="Duke Bloodstream Infection Biorepository"
     gene            1..1053
                     /locus_tag="WCU49_RS26355"
                     /old_locus_tag="WCU49_26355"
     CDS             1..1053
                     /locus_tag="WCU49_RS26355"
                     /old_locus_tag="WCU49_26355"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001557502.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001053268.1"
                     /translation="MNLQQRINKLPQLSSSFSFGKDIDNIHSFIFNETSKDKIEDLLRK
                     WVSGNQPCVFGKLASKKIKGLDFHLSIVNSPQLYNDDGHLFDFLRNERVRFKERARRGE
                     VSAHLIYFIHPQLAFARPSEELVDIQKYICSLHMPECYPIKEDVIYTESVPFQDKDGLK
                     IYKAGVNVFYSSAHRTRNHDRRIPGGILISVNAPGHFMRLAIEKGFYKDQEQALADIRN
                     MTIQSVGKGGYSHPEGISTTWHSESNLDRFGCPVHTGNSSYYSGFYHTDVLIPGELTKD
                     ERLLHEIENSDPMIFNWNVLFYVSLEEFPIDDPYYGEFIGIPVDDASMFFNSFQPRKFE
                     NKPLYEKEDD"
                     /name="hypothetical protein"
     gene            1055..1921
                     /locus_tag="WCU49_RS26360"
                     /old_locus_tag="WCU49_26360"
     CDS             1055..1921
                     /locus_tag="WCU49_RS26360"
                     /old_locus_tag="WCU49_26360"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335763.1"
                     /GO_function="GO:0005215 - transporter activity [Evidence
                     IEA]"
                     /GO_process="GO:0055085 - transmembrane transport [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DMT family transporter"
                     /protein_id="WP_001335763.1"
                     /translation="MIKGMLFAFLAAFSWGAAIVMSKKGVEELDAGGVFFWQICSAVIL
                     SWIVLFIKRKKLPLNSKAILAYATGVFEPFLAYTFTLYGLYFISAGSASIIFSLESVFI
                     LVLSVLICSVKINSPQYFILFLIGAIVGSILVALPDISNGSNNIVGYCLVVAGVLSAAF
                     YVVISSRLIKSFEPITLLSGQLTFSLILSSLFIFISKSSIYLPLESVIIVFSSGILQYF
                     LAFCFYLNSLRWLPVHLAGIMLYFIPLVALFLSWLFLDEQFTFLQGVGFIVTVLSVYFL
                     NRKYSEE"
                     /name="DMT family transporter"
     gene            complement(2896..3087)
                     /locus_tag="WCU49_RS26365"
                     /old_locus_tag="WCU49_26365"
     CDS             complement(2896..3087)
                     /locus_tag="WCU49_RS26365"
                     /old_locus_tag="WCU49_26365"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165975.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_000165975.1"
                     /translation="MTKQEKTALNMARFIRGQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENR"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3152..3475
                     /locus_tag="WCU49_RS26370"
                     /old_locus_tag="WCU49_26370"
     CDS             3152..3475
                     /locus_tag="WCU49_RS26370"
                     /old_locus_tag="WCU49_26370"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_000955999.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3684..>4115
                     /locus_tag="WCU49_RS26375"
                     /old_locus_tag="WCU49_26375"
                     /pseudo=""
     CDS             3684..>4115
                     /locus_tag="WCU49_RS26375"
                     /old_locus_tag="WCU49_26375"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            4153..4683
                     /locus_tag="WCU49_RS26380"
                     /old_locus_tag="WCU49_26380"
     CDS             4153..4683
                     /locus_tag="WCU49_RS26380"
                     /old_locus_tag="WCU49_26380"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_001673158.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTTALKELLERYQKTTVDTMDAHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILREQKESLEKLNAKTWGVRYHEDSNGRFLVLPKGMKAETNWTK
                     DNGKLNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            4690..4923
                     /locus_tag="WCU49_RS26385"
                     /old_locus_tag="WCU49_26385"
     CDS             4690..4923
                     /locus_tag="WCU49_RS26385"
                     /old_locus_tag="WCU49_26385"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137437.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWENAFVELQKMFSLTQRDNA
                     MLNGRVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          2305..2492
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          3466..5027
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgaatcttc aacaacgtat aaataaacta ccacaattat catccagttt ttcatttgga
       61 aaagatattg ataatattca ttcatttatc tttaacgaaa cttctaaaga taaaattgaa
      121 gatttactaa gaaaatgggt gtcaggcaat cagccctgtg tatttggtaa attggcaagc
      181 aagaaaatta aagggcttga tttccattta tctattgtaa atagccccca actatataat
      241 gatgatggtc atttgtttga ttttttgcgt aatgaaagag ttcgttttaa agaacgcgca
      301 agaagaggag aggtcagtgc gcatctcatt tattttattc atccacaact tgcctttgct
      361 cgtccatcag aagagttagt ggacatacaa aaatatattt gttcgctgca tatgccagag
      421 tgctatccaa taaaagagga tgttatttat actgaaagcg taccatttca ggataaagat
      481 gggctaaaaa tatataaggc tggtgttaat gttttttact cttctgctca tagaacaaga
      541 aatcatgata gaagaatacc agggggaata cttatttctg taaatgcccc ggggcatttt
      601 atgaggctgg cgatagaaaa aggtttctat aaagatcaag aacaagcgtt agcggatatt
      661 cgtaacatga ctattcagtc tgttggtaag ggtgggtatt cacatccgga agggatttct
      721 acaacatggc attcagaatc taatttggat cgttttggat gcccagtgca caccggtaat
      781 agttcttatt acagcggttt ttatcatact gatgtattaa ttccaggaga attaactaag
      841 gatgaaagat tgctccatga aatagaaaat agtgatccaa tgatcttcaa ctggaatgta
      901 ttgttttatg tttcattaga agagtttcct atagatgatc cttattatgg agagtttatt
      961 ggtattcctg tagatgatgc atctatgttt tttaactcct ttcaaccaag gaaatttgaa
     1021 aacaaacccc tttatgagaa agaggatgat taatatgatt aaaggaatgc tttttgcttt
     1081 tttagcagcg ttctcatggg gggcagctat cgtaatgagc aaaaaaggag ttgaagaact
     1141 agatgccgga ggggtgtttt tctggcagat ttgtagtgca gtaatactat cttggatagt
     1201 tctttttata aaaagaaaaa aactcccatt aaactcaaaa gcgatacttg cttatgcgac
     1261 aggcgttttt gaaccattct tagcgtatac ttttacactc tacggacttt attttatttc
     1321 agcaggaagc gcatcaatta ttttttcact tgaatcagtg tttatattgg tgttgtctgt
     1381 tcttatttgc tcagttaaaa ttaattcccc gcaatatttt atattgttcc ttataggtgc
     1441 aattgttggc agtattttgg tagccttgcc agacatcagt aatggatcga ataatattgt
     1501 tggatattgt cttgttgttg ccggtgtgtt atcggcagca ttttatgttg ttatatcgtc
     1561 tcgccttatt aaatcgtttg agcctatcac attattgagc ggacagttga cattctccct
     1621 tatactgtca tcgctcttta tttttatatc taaatcatca atttatcttc cgttggaatc
     1681 cgtgattatt gttttttcat ctggaatatt acaatatttt ttagcttttt gtttttactt
     1741 gaactccttg cgttggctcc cagttcattt ggcagggata atgttgtact ttattccgct
     1801 agttgcatta tttttgtcat ggttgttttt ggatgaacaa ttcacattct tacagggggt
     1861 aggatttatt gtaactgtgc taagtgtata ttttcttaac agaaaatact cagaggagta
     1921 acattctgtt caggattgcc ccccggcctc catcgatacc gtgccaaatg cacgtaaaaa
     1981 acgggagcgt ttctggtgtc ggaatgtaac caagggggtc agaggcgcgc taaaacgctc
     2041 tcaggggagt caaatagaga cgtttgtaac aaaaagatca aaggatcctc ttgagatcct
     2101 ttttttctgc gcgtaatctg ctgcctgtaa acgaaaaaac cgccttgcag ggcggtttga
     2161 tcgaaggtta agtcagcttg cagactgctt aaccaggtaa ctgtcttatg cgagacgagt
     2221 caccaaaatt gttcttctag tgtagccgca ctccggcagc cacttcaagt actctctaaa
     2281 tatctcgcac atgactttta ccaatggctg ctgccagtgg cgctttgtgg tgtcttttcc
     2341 gggttggacc caagagaaca gttaccggag aaggcgcagc agtcgggctg aacggggggt
     2401 tcctgcatac agcccagccc ggagcgaact gcctaagtcg ccccgagata ccagaagacg
     2461 tgagctatga gaaagcgcca cgtgtcccgt aagggagaaa ggcggaaaag gtatccggta
     2521 atcgatatgg cgggaacgtg ggggcgcagg agggagcgat tcaccggaaa cggtgatgat
     2581 ctttaagcca cgtcgggttt cgccaccgct ggcggatttc atggttgagc cgcaaggctc
     2641 ccacagatgc accgaaaaag tgtctgtttt gtgaagtccg tcaggggggc ggagcctatg
     2701 gaaaaagcgc ctccggcgcg gcctttcccg gggtttcgtt ttttgcgcag tatacactcc
     2761 gctatcgcta cgtgactggg tcagggcttc gccccgacac cccaaaggtc aacggcctga
     2821 cgcgccctgg cgggcttgtc tgctcccggc atccgctcac agacaagctg tgaccgtctc
     2881 cgggagctgc atgtgtcagc ggttttcacc gtcatccccg aagcgtgcga ggcaactgcg
     2941 gtaaagctca tcggcgtggt cgtgaagcga ttcacagatg tctgcctgtt catccgcgtc
     3001 cagttcgttg agcttctcca gcagcgttaa tgtctggcct ctgatgaagc gggccatgtt
     3061 aagggcggtt ttttcctgtt tggtcactga tgcctccgtg taaggggggg ttctgttcat
     3121 gggggtaatg ataccgatga aacgcgagag gatgctcacg atacgggtta ctgatgatga
     3181 acatgcccgg ttactggaac gctgtgaggg taaacaactg gcggtatgga tgcggcgggt
     3241 ctgcctgggt gagccggttg cccgttccgg gaagctgccg acactggcac cgccgttact
     3301 gcgtcagctg gccgccatcg ggaataacct taaccagaca gcgaggaagg tgaacagcgg
     3361 gcagtggtct tccggtgacc gggttcaggt ggtggccgca ctgatggcca tcggggatga
     3421 gctgcgccgg ctgcgtctgg cggtcaggga acagggggcg cgggatgata gttaagtttc
     3481 atgccagggg aaaaggtggt ggcagtggtc cggttgatta cctgctggga agggagcgta
     3541 accgggaagg ggcaacggtg cttcagggga atccggaaga ggtccgggaa ctcatcgatg
     3601 ccacgccatt tgcgaagaaa tacacgtcag gtgttctgtc gttcgcggag aaggagctgc
     3661 cgcctggagg gcgtgaaaaa gtgatggcga gctttgagcg tgtactgatg cccggtctcg
     3721 agaaaaatca gtacagcatc ctgtgggtgg agcaccagga caagggacgg cttgagctga
     3781 attttgtcat tccgaacatg gagctacaga ccggaaaacg cctccagccg tactacgacc
     3841 gggcagacag gccgagaatt gatgcctggc agacgctggt gaatcaccat tacggtctgc
     3901 atgaccccaa cgccccggag aaccgccgga cgctgaccct tcctgataac ctgccggaaa
     3961 cgaaacaggc gcttgctgag ggcgtcacac gcgggataga cgcgctttac catgccggag
     4021 agataaaagg ccgtcaggat gtgattcagg cgctcacaga ggcggggctt gaagtggtca
     4081 gggtgacgcg aagcagtatc agcattgcag acccgaacgg cgggaggaat atcagactga
     4141 aaggagcgtt ttatgagcaa tcttttacag acgggcgcgg agttcgagaa aaagctgaaa
     4201 gagagagccg aatctacaga gaaaatgctg aacgacgagt tcaggaagct cgaagaatct
     4261 gtaaacaggg aactgacctc aaacgaatct ttaatcagga acgctatcaa cgaccataca
     4321 acagccctga aagaactgct ggagaggtat cagaaaacga ccgtcgatac gatggacgcg
     4381 cactggaaaa ccgtactgaa aatgagcgtg aaacgctggc tgtggctgat tatcgtctca
     4441 gtactgatgt ttgccacgac cgggagtctg ctgtggtacc agggcatgaa gataaacgcg
     4501 aatatgaata ttctccgcga gcagaaagag agtctggaga agctgaacgc gaagacatgg
     4561 ggcgtgcgtt atcacgagga cagcaacgga cgttttctgg tgttgccgaa ggggatgaaa
     4621 gccgaaacga actggacgaa ggacaacggc aaactgaacg cagtgagact ggtgcaggag
     4681 tgacagagca tgacggagct ggaaagacat ttgctgaacg cattagagca actgcaacag
     4741 gactatatgc agcggctgaa cgaatgggag aacgccttcg tggaattgca gaaaatgttt
     4801 tcgcttacgc aacgggacaa cgcgatgctg aacgggcgag tcatgcagtt gagtcagcag
     4861 gtgcagcact tgagcgagcg gacagaacgc ttgagccagt tatacagcga gaacaggaga
     4921 taagggatga acggctgatg caggaacgcg aacatgagtt atctctggag cgggagcgtc
     4981 agccggaaat ccaggagcgg acactggatg gcccttcgct gggatggtga aaccatgaaa
     5041 aatgacgtgt tcagtggatt aaggcgggct aatgtggcct gtagcatctg gttgcatagg
     5101 tattcatgcg gttaaaattt atcaggtgcg atcgcggcag tttttcgggt ggtttgttgc
     5161 catttttacc tgtctgctgc cgtgatcgca ccgaacgcgt tttggcggtg cgtacaatgc
     5221 gacgttatgg taaatggagc ggattttcag gaaggagtga tactaacaac tcgaacactg
     5281 tgcaaataat gattttttta aaatatcggt aacgataata aattatttcg ttttacgccg
     5341 gtaataaata taatgtagtt tcagtatata aaaaaatata tgaggtgtct tgtgggagct
     5401 ttc
//
