LOCUS       NZ_CP147553             5631 bp    DNA     circular CON 05-APR-2024
DEFINITION  Escherichia coli strain GN04979 plasmid unnamed2, complete sequence.
ACCESSION   NZ_CP147553
VERSION     NZ_CP147553.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN40123756
            Assembly: GCF_037287395.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5631)
  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 5631)
  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_037287395.1-RS_2024_04_05
            Annotation Date                   :: 04/05/2024 19:20:29
            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)                     :: 5,394
            CDSs (total)                      :: 5,277
            Genes (coding)                    :: 5,037
            CDSs (with protein)               :: 5,037
            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)              :: 240
            CDSs (without protein)            :: 240
            Pseudo Genes (ambiguous residues) :: 0 of 240
            Pseudo Genes (frameshifted)       :: 94 of 240
            Pseudo Genes (incomplete)         :: 168 of 240
            Pseudo Genes (internal stop)      :: 44 of 240
            Pseudo Genes (multiple problems)  :: 59 of 240
            Pseudo Genes (short protein)      :: 4 of 240
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP147553.1.
            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..5631
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="GN04979"
                     /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="WCU06_RS26940"
                     /old_locus_tag="WCU06_26940"
     CDS             1..1053
                     /locus_tag="WCU06_RS26940"
                     /old_locus_tag="WCU06_26940"
                     /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="WCU06_RS26945"
                     /old_locus_tag="WCU06_26945"
     CDS             1055..1921
                     /locus_tag="WCU06_RS26945"
                     /old_locus_tag="WCU06_26945"
                     /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(3124..3315)
                     /locus_tag="WCU06_RS26950"
                     /old_locus_tag="WCU06_26950"
     CDS             complement(3124..3315)
                     /locus_tag="WCU06_RS26950"
                     /old_locus_tag="WCU06_26950"
                     /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            3380..3703
                     /locus_tag="WCU06_RS26955"
                     /old_locus_tag="WCU06_26955"
     CDS             3380..3703
                     /locus_tag="WCU06_RS26955"
                     /old_locus_tag="WCU06_26955"
                     /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            3912..>4343
                     /locus_tag="WCU06_RS26960"
                     /old_locus_tag="WCU06_26960"
                     /pseudo=""
     CDS             3912..>4343
                     /locus_tag="WCU06_RS26960"
                     /old_locus_tag="WCU06_26960"
                     /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            4381..4911
                     /locus_tag="WCU06_RS26965"
                     /old_locus_tag="WCU06_26965"
     CDS             4381..4911
                     /locus_tag="WCU06_RS26965"
                     /old_locus_tag="WCU06_26965"
                     /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            4918..5151
                     /locus_tag="WCU06_RS26970"
                     /old_locus_tag="WCU06_26970"
     CDS             4918..5151
                     /locus_tag="WCU06_RS26970"
                     /old_locus_tag="WCU06_26970"
                     /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          2949..3030
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          2305..2492
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          3694..5255
                     /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 ttttgcgcac atgttctttc
     2761 ctggtttatc cccgggttct gtggataaca gggttagcgt ttttgagaaa ggagagtccg
     2821 ctcgccgcag ccgaacgacc gagcgtagcg agtcagtgag cgaggaagcg gaagagcgcc
     2881 tgaactggca ttttctcctt acgcatctgt gcggcatttc acaccggaca tggcgcactt
     2941 ttcatacaat ccgcactgat gccgaatggt taagccagta tacactccgc tatcgctacg
     3001 tgactgggtc agggcttcgc cccgacaccc caaaggtcaa cggcctgacg cgccctggcg
     3061 ggcttgtctg ctcccggcat ccgctcacag acaagctgtg accgtctccg ggagctgcat
     3121 gtgtcagcgg ttttcaccgt catccccgaa gcgtgcgagg caactgcggt aaagctcatc
     3181 ggcgtggtcg tgaagcgatt cacagatgtc tgcctgttca tccgcgtcca gttcgttgag
     3241 cttctccagc agcgttaatg tctggcctct gatgaagcgg gccatgttaa gggcggtttt
     3301 ttcctgtttg gtcactgatg cctccgtgta agggggggtt ctgttcatgg gggtaatgat
     3361 accgatgaaa cgcgagagga tgctcacgat acgggttact gatgatgaac atgcccggtt
     3421 actggaacgc tgtgagggta aacaactggc ggtatggatg cggcgggtct gcctgggtga
     3481 gccggttgcc cgttccggga agctgccgac actggcaccg ccgttactgc gtcagctggc
     3541 cgccatcggg aataacctta accagacagc gaggaaggtg aacagcgggc agtggtcttc
     3601 cggtgaccgg gttcaggtgg tggccgcact gatggccatc ggggatgagc tgcgccggct
     3661 gcgtctggcg gtcagggaac agggggcgcg ggatgatagt taagtttcat gccaggggaa
     3721 aaggtggtgg cagtggtccg gttgattacc tgctgggaag ggagcgtaac cgggaagggg
     3781 caacggtgct tcaggggaat ccggaagagg tccgggaact catcgatgcc acgccatttg
     3841 cgaagaaata cacgtcaggt gttctgtcgt tcgcggagaa ggagctgccg cctggagggc
     3901 gtgaaaaagt gatggcgagc tttgagcgtg tactgatgcc cggtctcgag aaaaatcagt
     3961 acagcatcct gtgggtggag caccaggaca agggacggct tgagctgaat tttgtcattc
     4021 cgaacatgga gctacagacc ggaaaacgcc tccagccgta ctacgaccgg gcagacaggc
     4081 cgagaattga tgcctggcag acgctggtga atcaccatta cggtctgcat gaccccaacg
     4141 ccccggagaa ccgccggacg ctgacccttc ctgataacct gccggaaacg aaacaggcgc
     4201 ttgctgaggg cgtcacacgc gggatagacg cgctttacca tgccggagag ataaaaggcc
     4261 gtcaggatgt gattcaggcg ctcacagagg cggggcttga agtggtcagg gtgacgcgaa
     4321 gcagtatcag cattgcagac ccgaacggcg ggaggaatat cagactgaaa ggagcgtttt
     4381 atgagcaatc ttttacagac gggcgcggag ttcgagaaaa agctgaaaga gagagccgaa
     4441 tctacagaga aaatgctgaa cgacgagttc aggaagctcg aagaatctgt aaacagggaa
     4501 ctgacctcaa acgaatcttt aatcaggaac gctatcaacg accatacaac agccctgaaa
     4561 gaactgctgg agaggtatca gaaaacgacc gtcgatacga tggacgcgca ctggaaaacc
     4621 gtactgaaaa tgagcgtgaa acgctggctg tggctgatta tcgtctcagt actgatgttt
     4681 gccacgaccg ggagtctgct gtggtaccag ggcatgaaga taaacgcgaa tatgaatatt
     4741 ctccgcgagc agaaagagag tctggagaag ctgaacgcga agacatgggg cgtgcgttat
     4801 cacgaggaca gcaacggacg ttttctggtg ttgccgaagg ggatgaaagc cgaaacgaac
     4861 tggacgaagg acaacggcaa actgaacgca gtgagactgg tgcaggagtg acagagcatg
     4921 acggagctgg aaagacattt gctgaacgca ttagagcaac tgcaacagga ctatatgcag
     4981 cggctgaacg aatgggagaa cgccttcgtg gaattgcaga aaatgttttc gcttacgcaa
     5041 cgggacaacg cgatgctgaa cgggcgagtc atgcagttga gtcagcaggt gcagcacttg
     5101 agcgagcgga cagaacgctt gagccagtta tacagcgaga acaggagata agggatgaac
     5161 ggctgatgca ggaacgcgaa catgagttat ctctggagcg ggagcgtcag ccggaaatcc
     5221 aggagcggac actggatggc ccttcgctgg gatggtgaaa ccatgaaaaa tgacgtgttc
     5281 agtggattaa ggcgggctaa tgtggcctgt agcatctggt tgcataggta ttcatgcggt
     5341 taaaatttat caggtgcgat cgcggcagtt tttcgggtgg tttgttgcca tttttacctg
     5401 tctgctgccg tgatcgcacc gaacgcgttt tggcggtgcg tacaatgcga cgttatggta
     5461 aatggagcgg attttcagga aggagtgata ctaacaactc gaacactgtg caaataatga
     5521 tttttttaaa atatcggtaa cgataataaa ttatttcgtt ttacgccggt aataaatata
     5581 atgtagtttc agtatataaa aaaatatatg aggtgtcttg tgggagcttt c
//
