LOCUS       NZ_CP147537             4074 bp    DNA     circular CON 05-APR-2024
DEFINITION  Escherichia coli strain GN03551 plasmid unnamed2, complete sequence.
ACCESSION   NZ_CP147537
VERSION     NZ_CP147537.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN40123742
            Assembly: GCF_037269235.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4074)
  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 4074)
  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_037269235.1-RS_2024_04_05
            Annotation Date                   :: 04/05/2024 18:55:03
            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)                     :: 4,882
            CDSs (total)                      :: 4,769
            Genes (coding)                    :: 4,577
            CDSs (with protein)               :: 4,577
            Genes (RNA)                       :: 113
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 192
            CDSs (without protein)            :: 192
            Pseudo Genes (ambiguous residues) :: 0 of 192
            Pseudo Genes (frameshifted)       :: 72 of 192
            Pseudo Genes (incomplete)         :: 134 of 192
            Pseudo Genes (internal stop)      :: 33 of 192
            Pseudo Genes (multiple problems)  :: 43 of 192
            Pseudo Genes (short protein)      :: 4 of 192
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP147537.1.
            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..4074
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="GN03551"
                     /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..693
                     /locus_tag="WCU03_RS24400"
                     /old_locus_tag="WCU03_24400"
     CDS             1..693
                     /locus_tag="WCU03_RS24400"
                     /old_locus_tag="WCU03_24400"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /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_001281403.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCISRLKSGADAELQKT
                     MTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKNDEKREEFRWIQYRAQYAKG
                     EAKARITFSDAVMPYLTQLKGQFTRVVIKNISGLSSSYSIRIYEFLQQFRSTGERIIAL
                     NDFRSMLGIENKYKQFRDLNKILIKPCVDELNKKSDLAVTVETIKKGRTVVALHFRFKE
                     DKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(951..3110)
                     /gene="mobQ"
                     /locus_tag="WCU03_RS24405"
                     /old_locus_tag="WCU03_24405"
     CDS             complement(951..3110)
                     /gene="mobQ"
                     /locus_tag="WCU03_RS24405"
                     /old_locus_tag="WCU03_24405"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_338810610.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAECRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERSEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     gene            3289..3543
                     /gene="mobC"
                     /locus_tag="WCU03_RS24410"
                     /old_locus_tag="WCU03_24410"
     CDS             3289..3543
                     /gene="mobC"
                     /locus_tag="WCU03_RS24410"
                     /old_locus_tag="WCU03_24410"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091747.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     Typing          complement(2753..3111)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.056"
                     /coverage="100.0"
                     /evalue="3.94e-177"
     Typing          3112..3288
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.438"
                     /coverage="100.0"
                     /evalue="2.610000000000001e-86"
     Typing          2..693
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.965"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(955..3197)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.198"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgtcggact tgattgccta caagtcgaat gctttggttg aggccagcta caagttgacc
       61 ctacaggaac aacgttttct gttgctgtgt atcagtcgat tgaaatctgg tgctgatgct
      121 gaattgcaaa agacaatgac cattaccgct gcggaatatt ttgattcatt ccctgacatg
      181 gggcggaaaa atgccgaggt tcagttacag gaagcgatcg atcgtttatg ggacaggtcg
      241 atcattctca agaatgacga gaagcgtgag gagttccgct ggatccagta tcgggcacag
      301 tacgctaaag gtgaggccaa ggctcgaata accttttctg acgcggtaat gccttatctg
      361 acgcaactga aggggcaatt cacgcgcgtt gttataaaaa acatatcagg tttatcaagt
      421 agttacagta taagaatata cgagttcctc cagcaattcc gcagtacggg agagagaatt
      481 attgctctta atgactttcg ttcaatgtta gggattgaaa ataaatacaa acaattcaga
      541 gacttaaata aaatactaat aaaaccctgt gttgacgaac tgaacaaaaa aagcgacctg
      601 gctgtaacgg ttgagacgat caaaaagggg cgcacggttg tagccctgca ttttcgcttc
      661 aaggaagaca aacagatcaa gatgacgatc taaaatcgat tttaaggcac ctaaaacgct
      721 ccctgctgcg ttttttttgt gttagtagtg cgaaggtact attgaagtga aaaattgcgt
      781 caaaagcgct ctaatgcagc gaaaaaagaa cccccaattt ttgggggcgg aaaaacaaaa
      841 ctatgcttgc attatgtgtg tgtgcttctt gcattcatcc ctgtcgatga acatcgaaga
      901 acatcgacga acataacacg atgttaaaca aaacaaaata ttgttcacat tcactgtgac
      961 caaccgcgat catgtctcct ctcggtggtg tgtgttcttg catcttcctc gcgccgccat
     1021 tcatcccagg tacgattgaa acccagagag cggaacagat gatccggctg tttttctggt
     1081 gtgttgacgg cagcaaaaag cggtgcctca cgggttttca gatgaaactc cataagttcc
     1141 ggcgcaggtg atatgtggct gtctgcatcg tgatttacgg caacaccata ccctgcatac
     1201 cgtaacccct tatcggtcag tgcactgatg accagctggc tgttatcggc tgagggaacg
     1261 gcaaacgcgg gatacagcgt accattaagc cggacaacac cgcccagaga gtcatccacg
     1321 cccatgacca gcaaaagctg aagctggcgg gtttcccggt cgacagaact cattaccggc
     1381 atcagcgtcg gtagcagacg tccctgcgta aaatccacct tccttgctgc cagtgatggc
     1441 atggctggct ggcggtcttc tccaagacag aaagactccg gccatgtctt cggctggcgg
     1501 agattgcggg tatattgcgg ccatgtctgg caaacctgcg tcagaagttg ctcaaaggtc
     1561 gcagaggaat aaacacgttg cagtggtgga tgttgaccga tttcgcttcg gtcacagata
     1621 taaccactcc tgtcacgcat taaatcaaca cgctcaaaga ttctggtgcg gtatttctcc
     1681 agctcgttcc cccagagcgt gtattctccg ttccggttgt gaagcagaag gtaacaggtc
     1741 atttccccgt taccaggcat gggggcctcg ccataccccg taacgactgc gctcagtacc
     1801 cctgaatcca taacggcatt gtcatttttc ctgagctgtt ccgctcgtcg ctccgcgcga
     1861 ctacgttctg tatcctcctg ctccttccgg cgcaattcct cttcacgttt aagcaactgg
     1921 actctgagag ctgcaaggcc ggatgccccc cactgctgcc actgtttttc aaatgccgtc
     1981 tgactcgcgg gaatgtcctg tttctccacc ttccggtaat gctgtcgcaa tttttccatt
     2041 tgctggctca gcgactggat ttttccctgt tcgctacggt attccggtgc cgcccattgc
     2101 atcaggggaa tacgggaaaa accggacgaa aacggcgatg attttttcag gctggcagca
     2161 tggctcatcg cttcctttcg ttcggtgttc agctcttccc agcgtctgcg cgtcgcctgc
     2221 atatctgcca tcatcgacat ggcattactg gtgagtttcc atgccgcatt actgtccttc
     2281 ggcaacgctt cgatgatgtc acgtagtgtg tacgaagttg cgttgtcagg aagcacgata
     2341 ttcagaaggt cagccacacg gcgggcaggc tctgtcagcc cgctgttcct gagttcagtg
     2401 cgggaaatct gtatttccag gttaagcctg ttaatcagac gattctgttc gctgcgttct
     2461 gtttcgatac cgcgtgtttc catcgcacag gcagactttc cgaggtgaat accaggcgtt
     2521 ttctcaagcc cctgtcgctc gtatgaacga tggtctatct cttcctgata accggcgttc
     2581 gccagtgctc tgtttgcatg gtcagcccat gatgcacgcc acgtctcggc atgtgtccgg
     2641 tcgttccagt ccctgacctt tccgccgaac ccagcaggtc cgacagccct cgtggtcagc
     2701 atgatgtgcg catggggatt tgttttatcc atgtgatgga acgccacatc agcaatcatg
     2761 ccctgactga caaagttttc tctgacaaag gcgagaacgg tttcccgtgc ggcatcctgc
     2821 ggcagttcac gggggatagc gagttcaatt tcccgcgcaa gttgtgagtt cttccggcat
     2881 tcggccttct caacggcatt ccagagttcg gcacggttcg tacaccaggc aggggctgtc
     2941 gcgggggtca gaatcacagc ttcagccaca ccgcttttgc gggtgtagtc gtgagtcagt
     3001 ccggtacgct catcaagcat cagtgaaccg gaacgatagg cagcggaagc tacggcgctg
     3061 tagccgctgc ttctggagat aattttcatg ctgagatgat aaatcgccat ttctgccgta
     3121 atgccttttt gtagttttct ttcagccccg cagggcgcac acaatcgaaa cggagtggag
     3181 attgtataag tgcgcacttt gtgatttgtc gtgcattatg ccagctcagt ttttaaacta
     3241 ccagtgacgc gctaaaatgc gatttttcat cgcgcacgga gttacatcat gagcagaacg
     3301 ctcgaacaga agattgctga tgctgaggcg agattacagc gcctgaaggc gaagagccgg
     3361 agcctggaca cagcgcagaa ggttgttgtg ggtgcagcat tgctggcaaa ggtcagaaag
     3421 ccggaggagg tgcagttgcg tgcctggtta ctccagttcc tgaaggcaga ggtgacacga
     3481 caggctgatg tgacgcgcat actgccgctg attaacgagc tggaggcgct gccaggacag
     3541 tgattgtatc gtccgctcgc cgcagcccca gcgaccgagc gttagcgagc gagtgggcga
     3601 ggaagcggaa gtgaatccgt cgccaggttg agcacatacg cacggttttt cggtaggtga
     3661 tatgcgctga acccgcatga atactggatt tccacagggt tggaagggga gtagtcggaa
     3721 cttgcaattc tgctttcttg caacacattg tttttattgg ttttttgttt tcagcgcccc
     3781 aagttatcca caggctcgcc gttaagtttt tagatcttgt ttttaagatc ttgtttttaa
     3841 tacttgtttt agggtcaaaa ttcattaata aaatcaatat gttatagcgg tatatgtgga
     3901 ggaatttaag gtaaaggtgg aggaatttaa ggtgtttagg tggaggaatt taaggtaaag
     3961 gtggaggaat ttaaggtgtt attcacagaa atgtgaggat ataaaaaaaa atattccaca
     4021 tttcttattt gtggggcaca ttaaagcatc accacatttg aacgggatct ttgt
//
