LOCUS       NZ_CP147570             4109 bp    DNA     circular CON 05-APR-2024
DEFINITION  Escherichia coli strain GN02100 plasmid unnamed3, complete sequence.
ACCESSION   NZ_CP147570
VERSION     NZ_CP147570.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN40123764
            Assembly: GCF_037277815.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4109)
  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 4109)
  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_037277815.1-RS_2024_04_05
            Annotation Date                   :: 04/05/2024 19:16:31
            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)                     :: 5,207
            CDSs (total)                      :: 5,083
            Genes (coding)                    :: 4,879
            CDSs (with protein)               :: 4,879
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 96
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 204
            CDSs (without protein)            :: 204
            Pseudo Genes (ambiguous residues) :: 0 of 204
            Pseudo Genes (frameshifted)       :: 78 of 204
            Pseudo Genes (incomplete)         :: 135 of 204
            Pseudo Genes (internal stop)      :: 40 of 204
            Pseudo Genes (multiple problems)  :: 46 of 204
            Pseudo Genes (short protein)      :: 4 of 204
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP147570.1.
            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..4109
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="GN02100"
                     /isolation_source="bloodstream"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="unnamed3"
                     /geo_loc_name="USA: Durham"
                     /lat_lon="36.0070 N 78.9371 W"
                     /collected_by="Duke Bloodstream Infection Biorepository"
     gene            106..2265
                     /gene="mobQ"
                     /locus_tag="WCU26_RS26025"
                     /old_locus_tag="WCU26_26025"
     CDS             106..2265
                     /gene="mobQ"
                     /locus_tag="WCU26_RS26025"
                     /old_locus_tag="WCU26_26025"
                     /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_052940773.1"
                     /translation="MAIYHLSMKIISRSNGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILSPATAPAWCTNRTELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLSLEIQIFRTELRNSGLTEPARRVADLLNIELPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMTDMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTEFETQWQQWGASGLAALRAQL
                     LKREEELRRKELEDTERSRAERRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMT
                     SYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQHTRNLRQPKTWPEFFCLGEDRQPAMPSLAARKVDFTQGRLPPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNRHLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHATERRHDRGWSQ"
                     /name="mobQ"
     gene            complement(2514..3215)
                     /locus_tag="WCU26_RS26030"
                     /old_locus_tag="WCU26_26030"
     CDS             complement(2514..3215)
                     /locus_tag="WCU26_RS26030"
                     /old_locus_tag="WCU26_26030"
                     /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_000227989.1"
                     /translation="MVDLIAYKSNALVEASYKLTLQEQRFLLLCISRLQSGVDAPPPEL
                     QKTMTITAVEFFNSFPDMGRNHAEEKLQEAIDRLWDRSIILKDGEKREEFRWIQYRAQY
                     LKGEAKVQITFADAVMPYLTQLKGQFTKVVIKNISNLSKSYSIRIYEILQQFRNTGERM
                     ISLDDFRSMLQLEDKYKDFKTLNRALIKPAVAELNQKSDLAVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(3747..4037)
                     /locus_tag="WCU26_RS26035"
                     /old_locus_tag="WCU26_26035"
     CDS             complement(3747..4037)
                     /locus_tag="WCU26_RS26035"
                     /old_locus_tag="WCU26_26035"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001514113.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000091756.1"
                     /translation="MSRTLEQKIAEAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVSRIQPLIDELNALPKPVPKGVSKNGQQA"
                     /name="hypothetical protein"
     Typing          complement(10..105)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="95.876"
                     /coverage="95.0"
                     /evalue="2.8e-36"
     Typing          106..464
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.222"
                     /coverage="100.0"
                     /evalue="3.97e-172"
     Typing          20..2262
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.791"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgcgcagaa atcacgaagt gcgcacttat acaatctcac cttcggttcg attgtgtgcg
       61 ccctgcgggg ctgaaagaaa actgcaaaaa ggcattacgg cagaaatggc gatttatcat
      121 ctcagcatga aaatcatctc cagaagcaac ggctacagcg ccgttgcttc tgctgcctat
      181 cgttccggtt cactaatgct tgatgagcgt accggactga ctcacgacta cacccgcaaa
      241 agcggtgtgg ctgaggctgt gattctgtcc cccgccaccg cccctgcctg gtgtacgaac
      301 cgtaccgaac tctggaatgc cgttgagaag gccgaacgtc ggaagaactc acaacttgcg
      361 cgggaaattg aactcgccat cccccgtgaa ctgccgcagg atgccgcacg ggaaaccgtt
      421 ctcgcctttg tcagagaaaa ctttgtcagt cagggcatga ttgctgatgt ggcgttccat
      481 cacatggata aaacaaatcc ccatgcgcac atcatgctga ccacgagggc tgtcggacct
      541 gcggggttcg gtggaaaggt cagggactgg aacgaccgga cacatgccga gacgtggcgg
      601 gcatcatggg ctgaccatgc aaacagggca ctggcgaacg ccggttatca ggaagagata
      661 gaccatcgtt catacgagcg acaggggctt gagaaaacgc ctggtattca cctcggaaag
      721 tctgcctgtg cgatggaaac acgcggtatc gaaacagaac gcggcgaaca gaatcgtctg
      781 attaacaggc ttagcctgga aatacagatt ttccgtaccg aactcaggaa cagcgggctg
      841 acagagcctg cccgccgtgt ggctgacctt ctgaatattg agcttcctga caacgcaact
      901 tcgtacacac tacgtgacat catcgaagcg ttgccgaagg acagtaacgc ggcatggaaa
      961 ctcaccagta atgccatgtc gatgatgaca gatatgcagg cgacgcgcag acgctgggaa
     1021 gagctgaaca ccgaacgaaa ggaagcgatg agccatgctg ccagcctgaa aaaatcatcg
     1081 ccgttttcgt ccggtttttc ccgtattccc ctgatgcaat gggctgcacc ggaataccgt
     1141 agtgagcagg gaaaaattca gtctctgagc cagcaaatgg aaaaattgcg acagcattac
     1201 cggaaggtgg agaaacagga cattcccgcg agtcagacgg aatttgaaac acagtggcag
     1261 cagtgggggg catccggcct tgcagctctc agagcccagt tgcttaaacg tgaagaggaa
     1321 ttgcgccgga aggagctgga ggatacagaa cgtagtcgcg cggagcgacg agcggagcag
     1381 ctcaggaaaa atgacaatgc cgttatggat tcaggggtac tgagagcagt cgttacgggg
     1441 tatggcgagg cccccatgcc tggtaacggg gaaatgacca gttaccttct gcttcacaac
     1501 cggaacggag aatatacgct ctgggggaac gagctggaga aataccgcac cagaatcttt
     1561 gagcgtgttg atttaatgcg tgacaggagt ggttatatct gtgaccgaag cgaaatcggt
     1621 caacatccac cattgcaacg tgtttattcc tctgcgacct ttgagcaact gctgacgcag
     1681 gtttgccaga catggccaca acatacccgc aatctccgcc agccgaagac atggccggag
     1741 tttttctgtc ttggagaaga ccgccagcca gccatgccat cactggcagc aaggaaggtg
     1801 gattttacgc agggacgtct gccaccgacg ctgatgccgg taatgagttc tgtcgaccgg
     1861 gaaacccgcc agcttcagct tttgctggtc atgggcgtgg atgactctct gggcggcgtt
     1921 gtccggctta atggcacgct gtatcccgcg tttgccgttc cctcagccga taacaggcat
     1981 ctggtcatca gtgcgctgac ggacaagggg ttacggtatg cagggtatgg tgttgccgtc
     2041 aatcacgatg cagacagcca catatcacct gcaccggaac ttatggagtt tcatctgaaa
     2101 acccgtgagg caccgctttt tgctgccgtc aatacaccag aaaaacagcc ggatcatctg
     2161 ttccgctcgc tgggttttaa tcgtacctgg gacgaatggc ggcgcgagga agatgcacga
     2221 acacacgcca ccgagaggag gcacgatcgc ggttggtcac agtgaatgtg cacaatattt
     2281 tgttttgttt aacatcatgt tatgttcatg tgacgttcac agacagggat gaacgtcaat
     2341 aagcacacac aacaaactag ataatctccg catagtttct tccccccgca tatgggggat
     2401 ttttttagct cgtgagagcg attctgacga tgtttttgtg attcgtagta ccatcgcata
     2461 ccttacacaa aaaaaacgcg tcagcgcgcg ttttagatgc cttagaatcg attttagatc
     2521 gtcatcttga tctgtttgtc ttccttgaag cgaaaatgca gggctacgac agtgcgcccc
     2581 ttcttgattg tctcaaccgt tacggccaga tcgctttttt gattcagttc cgccactgcc
     2641 ggttttatga gggctctatt taacgtcttg aaatctttat atttatcttc cagttgtagc
     2701 atgctgcgga aatcatctag agaaatcatc cgctcccctg tgttacggaa ctgttggagg
     2761 atttcgtata ttctgatgct ataactcttt gataaattag atatgttttt aattacaact
     2821 tttgtgaatt gcccttttaa ttgcgttaag tacggcatta cagcatctgc gaaagttatt
     2881 tgaacttttg cttcgccttt caggtactgc gcccgatact ggatccaacg gaactcctcg
     2941 cgtttttcac catccttaag aatgatcgac ctgtcccaca gacgatcgat cgcttcctgt
     3001 aacttttctt cggcatggtt tcttcccatg tcaggaaatg aattaaaaaa ctccacagcc
     3061 gtaatagtca tggtcttttg taattcaggt ggaggagcat caacacctga ctgtaatcga
     3121 ctaatgcaca gcaacaggaa acgctgctcc tgtaacgtga gcttgtagct ggcttcgact
     3181 aaggcattgg atttgtaagc tatcaaatca accattgagc accctcacct aaagtaaact
     3241 aaaaaaaaac tagttcaccc catcaattgg tgcaatcatt tttttttaat tcaccatttt
     3301 ctgtggataa ccacccccga aatgttcacc tttacccccg aaatgttcac ctaaccaccc
     3361 ccgaaatgtt cacctttacc cccgaaatgt tcacctatag caatctaatc ccttgaattc
     3421 cataagaaat ttcggtccga aaacaagtat taaaaacaag atcttaaaaa caagatctaa
     3481 aaacttaacg gcgagcctgt ggaaaactcg gggtgcgcaa aacaaaaacc catgaaaaac
     3541 agcaagttac aaaaaagcag aacagcagac actggcaaaa cgctgttcaa ccctgtggaa
     3601 aaccagtatt catgcgggtt gaacggctat caccaactga gcatcggcgc gtaagtgccc
     3661 tgttttggtg cagcagcttt tccgcttcct cgcccactcg ctcgctaacg ctcggtcgct
     3721 ggggctgcgg cgagcggatg gtgcattcac gcctgctggc cgttttttga cacgcctttg
     3781 gggacgggtt ttggcaacgc gttcagttcg tcaatcaacg gctgtatcct gctcacatca
     3841 gcctgccgtg tcacctctgc cttcaggaac tggagtaacc aggcgcgcaa ttgcacctcc
     3901 tccggctttc tgacctttgc cagcaatgca gcacctacaa cgaccttctg cgctgtgtcc
     3961 aggctccggc tctttgcctt cagacgctgc aatctggctt cagcttcggc aattttctgt
     4021 tcgagtgttc tgctcatgat gtaactccgt gcgcggtgaa aaatcgcatt ttagctcgtc
     4081 actggtagtt taaaaactga gctggcata
//
