LOCUS       NZ_CP147534             4074 bp    DNA     circular CON 05-APR-2024
DEFINITION  Escherichia coli strain GN03139 plasmid unnamed2, complete sequence.
ACCESSION   NZ_CP147534
VERSION     NZ_CP147534.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN40123741
            Assembly: GCF_037231045.1
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_037231045.1-RS_2024_04_05
            Annotation Date                   :: 04/05/2024 19:06:03
            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)                     :: 4,852
            CDSs (total)                      :: 4,739
            Genes (coding)                    :: 4,558
            CDSs (with protein)               :: 4,558
            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)              :: 181
            CDSs (without protein)            :: 181
            Pseudo Genes (ambiguous residues) :: 0 of 181
            Pseudo Genes (frameshifted)       :: 69 of 181
            Pseudo Genes (incomplete)         :: 125 of 181
            Pseudo Genes (internal stop)      :: 32 of 181
            Pseudo Genes (multiple problems)  :: 41 of 181
            Pseudo Genes (short protein)      :: 4 of 181
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP147534.1.
            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="GN03139"
                     /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..2160
                     /gene="mobQ"
                     /locus_tag="WCU35_RS24250"
                     /old_locus_tag="WCU35_24250"
     CDS             1..2160
                     /gene="mobQ"
                     /locus_tag="WCU35_RS24250"
                     /old_locus_tag="WCU35_24250"
                     /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            complement(2418..3110)
                     /locus_tag="WCU35_RS24255"
                     /old_locus_tag="WCU35_24255"
     CDS             complement(2418..3110)
                     /locus_tag="WCU35_RS24255"
                     /old_locus_tag="WCU35_24255"
                     /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(3642..3896)
                     /gene="mobC"
                     /locus_tag="WCU35_RS24260"
                     /old_locus_tag="WCU35_24260"
     CDS             complement(3642..3896)
                     /gene="mobC"
                     /locus_tag="WCU35_RS24260"
                     /old_locus_tag="WCU35_24260"
                     /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          2..359
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.05"
                     /coverage="99.0"
                     /evalue="1.4199999999999999e-176"
     Typing          complement(3898..4074)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.438"
                     /coverage="100.0"
                     /evalue="2.610000000000001e-86"
     Typing          complement(2419..3110)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.965"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2..2157
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.444"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atggcgattt atcatctcag catgaaaatt atctccagaa gcagcggcta cagcgccgta
       61 gcttccgctg cctatcgttc cggttcactg atgcttgatg agcgtaccgg actgactcac
      121 gactacaccc gcaaaagcgg tgtggctgaa gctgtgattc tgacccccgc gacagcccct
      181 gcctggtgta cgaaccgtgc cgaactctgg aatgccgttg agaaggccga atgccggaag
      241 aactcacaac ttgcgcggga aattgaactc gctatccccc gtgaactgcc gcaggatgcc
      301 gcacgggaaa ccgttctcgc ctttgtcaga gaaaactttg tcagtcaggg catgattgct
      361 gatgtggcgt tccatcacat ggataaaaca aatccccatg cgcacatcat gctgaccacg
      421 agggctgtcg gacctgctgg gttcggcgga aaggtcaggg actggaacga ccggacacat
      481 gccgagacgt ggcgtgcatc atgggctgac catgcaaaca gagcactggc gaacgccggt
      541 tatcaggaag agatagacca tcgttcatac gagcgacagg ggcttgagaa aacgcctggt
      601 attcacctcg gaaagtctgc ctgtgcgatg gaaacacgcg gtatcgaaac agaacgcagc
      661 gaacagaatc gtctgattaa caggcttaac ctggaaatac agatttcccg cactgaactc
      721 aggaacagcg 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 cggggtatgg 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 cgtctgctac 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 ctctctgggt ttcaatcgta cctgggatga atggcggcgc
     2101 gaggaagatg caagaacaca caccaccgag aggagacatg atcgcggttg gtcacagtga
     2161 atgtgaacaa tattttgttt tgtttaacat cgtgttatgt tcgtcgatgt tcttcgatgt
     2221 tcatcgacag ggatgaatgc aagaagcaca cacacataat gcaagcatag ttttgttttt
     2281 ccgcccccaa aaattggggg ttcttttttc gctgcattag agcgcttttg acgcaatttt
     2341 tcacttcaat agtaccttcg cactactaac acaaaaaaaa cgcagcaggg agcgttttag
     2401 gtgccttaaa atcgatttta gatcgtcatc ttgatctgtt tgtcttcctt gaagcgaaaa
     2461 tgcagggcta caaccgtgcg cccctttttg atcgtctcaa ccgttacagc caggtcgctt
     2521 tttttgttca gttcgtcaac acagggtttt attagtattt tatttaagtc tctgaattgt
     2581 ttgtatttat tttcaatccc taacattgaa cgaaagtcat taagagcaat aattctctct
     2641 cccgtactgc ggaattgctg gaggaactcg tatattctta tactgtaact acttgataaa
     2701 cctgatatgt tttttataac aacgcgcgtg aattgcccct tcagttgcgt cagataaggc
     2761 attaccgcgt cagaaaaggt tattcgagcc ttggcctcac ctttagcgta ctgtgcccga
     2821 tactggatcc agcggaactc ctcacgcttc tcgtcattct tgagaatgat cgacctgtcc
     2881 cataaacgat cgatcgcttc ctgtaactga acctcggcat ttttccgccc catgtcaggg
     2941 aatgaatcaa aatattccgc agcggtaatg gtcattgtct tttgcaattc agcatcagca
     3001 ccagatttca atcgactgat acacagcaac agaaaacgtt gttcctgtag ggtcaacttg
     3061 tagctggcct caaccaaagc attcgacttg taggcaatca agtccgacat acaaagatcc
     3121 cgttcaaatg tggtgatgct ttaatgtgcc ccacaaataa gaaatgtgga atattttttt
     3181 ttatatcctc acatttctgt gaataacacc ttaaattcct ccacctttac cttaaattcc
     3241 tccacctaaa caccttaaat tcctccacct ttaccttaaa ttcctccaca tataccgcta
     3301 taacatattg attttattaa tgaattttga ccctaaaaca agtattaaaa acaagatctt
     3361 aaaaacaaga tctaaaaact taacggcgag cctgtggata acttggggcg ctgaaaacaa
     3421 aaaaccaata aaaacaatgt gttgcaagaa agcagaattg caagttccga ctactcccct
     3481 tccaaccctg tggaaatcca gtattcatgc gggttcagcg catatcacct accgaaaaac
     3541 cgtgcgtatg tgctcaacct ggcgacggat tcacttccgc ttcctcgccc actcgctcgc
     3601 taacgctcgg tcgctggggc tgcggcgagc ggacgataca atcactgtcc tggcagcgcc
     3661 tccagctcgt taatcagcgg cagtatgcgc gtcacatcag cctgtcgtgt cacctctgcc
     3721 ttcaggaact ggagtaacca ggcacgcaac tgcacctcct ccggctttct gacctttgcc
     3781 agcaatgctg cacccacaac aaccttctgc gctgtgtcca ggctccggct cttcgccttc
     3841 aggcgctgta atctcgcctc agcatcagca atcttctgtt cgagcgttct gctcatgatg
     3901 taactccgtg cgcgatgaaa aatcgcattt tagcgcgtca ctggtagttt aaaaactgag
     3961 ctggcataat gcacgacaaa tcacaaagtg cgcacttata caatctccac tccgtttcga
     4021 ttgtgtgcgc cctgcggggc tgaaagaaaa ctacaaaaag gcattacggc agaa
//
