LOCUS       NZ_CP147530             4087 bp    DNA     circular CON 05-APR-2024
DEFINITION  Escherichia coli strain GN05056 plasmid unnamed1, complete sequence.
ACCESSION   NZ_CP147530
VERSION     NZ_CP147530.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN40123740
            Assembly: GCF_037225585.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4087)
  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 4087)
  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_037225585.1-RS_2024_04_05
            Annotation Date                   :: 04/05/2024 19:21:29
            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)                     :: 5,154
            CDSs (total)                      :: 5,041
            Genes (coding)                    :: 4,816
            CDSs (with protein)               :: 4,816
            Genes (RNA)                       :: 113
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 225
            CDSs (without protein)            :: 225
            Pseudo Genes (ambiguous residues) :: 0 of 225
            Pseudo Genes (frameshifted)       :: 81 of 225
            Pseudo Genes (incomplete)         :: 166 of 225
            Pseudo Genes (internal stop)      :: 42 of 225
            Pseudo Genes (multiple problems)  :: 57 of 225
            Pseudo Genes (short protein)      :: 3 of 225
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP147530.1.
            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..4087
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="GN05056"
                     /isolation_source="bloodstream"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="unnamed1"
                     /geo_loc_name="USA: Durham"
                     /lat_lon="36.0070 N 78.9371 W"
                     /collected_by="Duke Bloodstream Infection Biorepository"
     gene            1..2160
                     /gene="mobQ"
                     /locus_tag="WCU48_RS25200"
                     /old_locus_tag="WCU48_25200"
     CDS             1..2160
                     /gene="mobQ"
                     /locus_tag="WCU48_RS25200"
                     /old_locus_tag="WCU48_25200"
                     /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_338822349.1"
                     /translation="MAIYHLSMKIISRNSGYSAVASAAYRSGSLMLDERTGLTHDYTCK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTEYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLATL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHATERRHDRGWSQ"
                     /name="mobQ"
     gene            complement(2416..3124)
                     /locus_tag="WCU48_RS25205"
                     /old_locus_tag="WCU48_25205"
                     /pseudo=""
     CDS             complement(2416..3124)
                     /locus_tag="WCU48_RS25205"
                     /old_locus_tag="WCU48_25205"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001296720.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     gene            complement(3656..3910)
                     /gene="mobC"
                     /locus_tag="WCU48_RS25210"
                     /old_locus_tag="WCU48_25210"
     CDS             complement(3656..3910)
                     /gene="mobC"
                     /locus_tag="WCU48_RS25210"
                     /old_locus_tag="WCU48_25210"
                     /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_000091745.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     Typing          2..359
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.721"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(3912..4087)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.438"
                     /coverage="100.0"
                     /evalue="9.4e-86"
     Typing          complement(2417..3124)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.859"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2..2157
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.583"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atggcgattt atcatctcag catgaaaatc atctccagaa acagcggcta cagcgccgtt
       61 gcttctgctg cctatcgttc cggttcactg atgcttgatg agcgtaccgg actgactcac
      121 gactacacct gcaaaagcgg tgtggctgaa gctgtgattc tgactcccgc gacagcccct
      181 gcctggtgta cgaaccgtgc cgaactctgg aatgccgttg agaaggccga acgccggaag
      241 aactcacaac ttgcgcggga aattgaactc gccatccccc gcgaactacc gcaggatgcc
      301 gcacgggaaa ccgttctcgc ctttgtcaga gaaaactttg tcagtcaggg catgattgct
      361 gatgtggcgt tccatcacat ggataaaaca aatccccatg cgcacatcat gctgaccacg
      421 agagctgtcg gacctgctgg attcggtgga aaggtcaggg actggaacga ccggacacat
      481 gccgagacgt ggcgtgcatc atgggctgac catgcgaaca gggcactggc gaacgccggt
      541 tatcaggaag agatagacca tcgttcatac gagcgacagg ggcttgagaa aacgcctggt
      601 attcacctcg gaaagtctgc ctgtgcgatg gaaacacgcg gtatcgaaac agaacgcggc
      661 gaacagaatc gtctgattaa cagacttaac ctggaaatac agatttcccg taccgaactc
      721 agaaacagcg ggctgacaga gcctgcccgc cgtgtggctg accttctgaa tatcgtgctt
      781 cctgacaacg caacttcgta cacactacgt gacatcatcg aagcgttgcc gaaggacagt
      841 aatgcggcat ggaaactcac cagtaatgcc atgtcgatga tggcagatat gcaggcgacg
      901 cgcagacgct gggaagagct gaacaccgaa cgaaaggaag cgatgagcca tgctgccagc
      961 ctgaaaaaat catcgccgtt ttcgtccggt ttttcccgta ttcccctgat gcaatgggcg
     1021 gcaccggaat accgtagcga acagggaaaa atccagtcgc tgagccagca aatggaaaaa
     1081 ttgcgacagc attaccggaa ggtggagaaa caggacattc ccgcgagtca gacggcattt
     1141 gaaaaacagt ggcagcagtg gggggcatcc ggccttgcag ctctcagagt ccagttgctt
     1201 aaacgtgaag aggaattgcg ccggaaggag caggaggata cagaacgtag tcgcgcggag
     1261 cgacgagcgg aacagctcag gaaaaatgac aatgccgtta tggattcagg ggtactgagc
     1321 gcagtcgtta cggagtatgg cgaggccccc atgcctggta acggggaaat gacctgttac
     1381 cttctgcttc acaaccggaa cggagaatac acgctctggg ggaacgagct ggagaaatac
     1441 cgcaccagaa tctttgagcg tgttgattta atgcgtgaca ggagtggtta tatctgtgac
     1501 cgaagcgaaa tcggtcaaca tccaccactg caacgtgttt attcctctgc gacctttgag
     1561 caacttctga cgcaggtttg ccagacatgg ccgcaatata cccgcaatct ccgccagccg
     1621 aagacatggc cggagtcttt ctgtcttgga gaagaccgcc agccagccat gccatcactg
     1681 gcagcaagga aggtggattt tacgcaggga cgtctgctag cgacgctgat gccggtaatg
     1741 agttctgtcg accgggaaac ccgccagctt cagcttttgc tggtcatggg cgtggatgac
     1801 tctctgggcg gtgttgtccg gcttaatggt acgctgtatc ccgcgtttgc cgttccctca
     1861 gccgataaca gccagctggt catcagtgca ctgaccgata aggggttacg gtatgcaggg
     1921 tatggtgttg ccgtaaatca cgatgcagac agccacatat cacctgcgcc ggaacttatg
     1981 gagtttcatc tgaaaacccg tgaggcaccg ctttttgctg ccgtcaacac accagaaaaa
     2041 cagccggatc atctgttccg ctcgctgggt tttaatcgta cctgggacga atggcggcgc
     2101 gaggaagatg cacgaacaca cgccaccgag aggagacatg atcgcggttg gtcacagtga
     2161 atgtgaacaa tattttgttt tgtttaacat cgtgttatgt tcgtcgatgt tcttcgatgt
     2221 tcatcgacag ggatgaatgc aagaagcaca cacataatgc aagcatagtt ttgtttttcc
     2281 gcccccgaaa aatgggggtt cttttttcgc tgcattagag cgcttttgac gcaatttttc
     2341 acttcaatag taccttcgca ctactaacac aaaaaaaacg cagcagggag cgttttaggt
     2401 gccttaaaat cgattctaga tcgtcatctt gatctgtttg tcttccttga agcgaaaatg
     2461 cagggctaca accgtgcgcc cctttttgat cgtctcaacc ggttacagcc aggtcgcttt
     2521 ttttgttcag ttcgtcaaca cagggtttta ttagatccct gtttaacgtt ttgaaatctt
     2581 tatatttacc atcaagcatc agtgatgatt taaaatcatc gagggcgata atacgttccc
     2641 cagtactgcg gaattgctgg agaatttcgt atattcttat gctgtaactt cttgataaat
     2701 tagaaatatt tttaatgacg actctggtga attgcccctt caactgtgtc agataaggca
     2761 ttaccgcgtc agaaaaagtg atttgtgctt tcccctctcc cctcgcgtac tgtgcccgat
     2821 actgaatcca gcggaactcc tcgcgcttct cgtcgtcctt gagaatgatc gacctgtccc
     2881 acaaacgatc gatcgcttcc tgtagctgaa cctcggcatt tttccgcccc atatcaggga
     2941 atgaatcaaa atattccgca gctgtaatgg tcattgtctt ttgcaattca ggtgaagcta
     3001 cgtcagtacc ggagttaagt cggcttatgc agagcaataa gaaacgctgt tcttgtaaag
     3061 ttagcttgta actggcctca accagcgcat tggacttata ggctatcaga gggtttgatg
     3121 tcattttaac caccaggcca aaaatgaggt gaaataaaaa cctatcacct ttagcattgg
     3181 tgagcaatta tattttcacc ccccattttc ctgtgaatat taccttaaat ctcctcacct
     3241 ttaccttaaa ttacctcacc caagcacctt aaattatatc acctttacct taaatcatat
     3301 cacctatagc gttgtaacat tttgttttct ataaggaatt ttggcgctaa aacaagtatt
     3361 aaaaacaaga tcttaaaaac aagatctaaa aacttaacga cgagcctgtg gataacttgg
     3421 agtgctgaaa acaaaaaacc aataaaaaca atgcgttgca aaaaagcaga attgcaagtt
     3481 ccgaatacac cccctccaac cctgtggaaa tccagtattc atgcgggttc agcgcatatc
     3541 acctcccgaa aaaccgtgcg tatgtgctca atcaggcgac ggattcactt ccgcttcctc
     3601 gcccactcgc tcgctaacgc tcggtcgctg ggactgcggc gagcggacga tacaatcact
     3661 gtcctggcag cgcttccagc tcgttaatca gcggcagtat gcgcgtcaca tcagcctgtc
     3721 gtgtcacctc tgccttcagg aactggagta accaggcacg caactgcacc tcctccggct
     3781 ttctgacctt tgccagcaat gctgcaccca caatgacctt ctgcgctgtg tccagactcc
     3841 tgctcttcgc cttcaggcgc tgtaatctgg cctcagcatc agcaatcttc tgttcgagtg
     3901 ttctgctcat gatgtaactc cgtgcgcgat gaaaaatcgc attttagcgc gtcactggta
     3961 gtttaaaaac tgagctggca taatgcacgg aaaatcacga atgcgcactt atacaatctc
     4021 cactccgttt cgattgtgtg cgccctgcgg ggctgaaaga aaaccacaaa aaggcattac
     4081 ggcagaa
//
