LOCUS       NZ_CP147589             5153 bp    DNA     circular CON 05-APR-2024
DEFINITION  Escherichia coli strain GN06667 plasmid unnamed4, complete sequence.
ACCESSION   NZ_CP147589
VERSION     NZ_CP147589.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN40123769
            Assembly: GCF_037280675.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5153)
  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 5153)
  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_037280675.1-RS_2024_04_05
            Annotation Date                   :: 04/05/2024 19:09:56
            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)                     :: 5,102
            CDSs (total)                      :: 4,979
            Genes (coding)                    :: 4,766
            CDSs (with protein)               :: 4,766
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 95
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 213
            CDSs (without protein)            :: 213
            Pseudo Genes (ambiguous residues) :: 0 of 213
            Pseudo Genes (frameshifted)       :: 83 of 213
            Pseudo Genes (incomplete)         :: 136 of 213
            Pseudo Genes (internal stop)      :: 42 of 213
            Pseudo Genes (multiple problems)  :: 43 of 213
            Pseudo Genes (short protein)      :: 3 of 213
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP147589.1.
            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..5153
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="GN06667"
                     /isolation_source="bloodstream"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="unnamed4"
                     /geo_loc_name="USA: Durham"
                     /lat_lon="36.0070 N 78.9371 W"
                     /collected_by="Duke Bloodstream Infection Biorepository"
     gene            complement(241..435)
                     /locus_tag="WCU01_RS25455"
                     /old_locus_tag="WCU01_25455"
     CDS             complement(241..435)
                     /locus_tag="WCU01_RS25455"
                     /old_locus_tag="WCU01_25455"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041639.1"
                     /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_001041621.1"
                     /translation="MNKQQQAVLNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA
                     EELQNSIQTRFEVENSTER"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            719..1042
                     /gene="mobA"
                     /locus_tag="WCU01_RS25460"
                     /old_locus_tag="WCU01_25460"
     CDS             719..1042
                     /gene="mobA"
                     /locus_tag="WCU01_RS25460"
                     /old_locus_tag="WCU01_25460"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_000166966.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            complement(1267..1686)
                     /locus_tag="WCU01_RS25465"
                     /old_locus_tag="WCU01_25465"
     CDS             complement(1267..1686)
                     /locus_tag="WCU01_RS25465"
                     /old_locus_tag="WCU01_25465"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016247941.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Exc2 family lipoprotein"
                     /protein_id="WP_001254967.1"
                     /translation="MRRTGNKLCLIAMITATVALTACTPKGSVEQHTRHYVYASDDGFD
                     PNFSTQKADTTRMMVPFFRQFWDMGAKDKATGKSRSDVQQRIQQFHSQEFLNSLRGTTQ
                     FAGTDYRSKDLTPKKSRLLADTISAVYLDGYEGRQ"
                     /name="Exc2 family lipoprotein"
     gene            complement(1767..2204)
                     /locus_tag="WCU01_RS25470"
                     /old_locus_tag="WCU01_25470"
     CDS             complement(1767..2204)
                     /locus_tag="WCU01_RS25470"
                     /old_locus_tag="WCU01_25470"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001749514.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001318234.1"
                     /translation="MGHCNFMAWHTLRDALKMTGRSRSQFYRDMRSGLVSYRTSQDGRR
                     EFETSELIRAYGELKRNETPERHTQGHSEKPHDQQTERILRELNELKQCLTLMLEDKQA
                     QDTERRRQEAERKQLQNEIAQLRQALEQEKKRGFWSRLFGH"
                     /name="hypothetical protein"
     gene            2464..4029
                     /locus_tag="WCU01_RS25475"
                     /old_locus_tag="WCU01_25475"
     CDS             2464..4029
                     /locus_tag="WCU01_RS25475"
                     /old_locus_tag="WCU01_25475"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000447006.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_function="GO:0140911 - pore-forming activity [Evidence
                     IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA];
                     GO:0050829 - defense response to Gram-negative bacterium
                     [Evidence IEA]; GO:0031640 - killing of cells of another
                     organism [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin-like pore-forming protein"
                     /protein_id="WP_000447003.1"
                     /translation="METAVAYYKDGVPYDDKGQVIITLLNGNPDGSGSGGGGGTGGSKS
                     ESSAAIHATAKWSTAQLKKTQAEQAARAKAAAEAQAKAKANRDALTQHLKDIVNEALRH
                     NSTHPEVIDLAHANNAAMQAEAERLRLAKAEEKARKEAEAAEKAFQEAEQRRKEIEKEQ
                     AETERQLKLAEDEEKRLAALSEEARAVEVAQKNLAAAQSELAKVDEEINTLNTRLSSSI
                     HARDAETNTLSGKRNELDQASAKYKELDERVKLLSPRANDPLQSRPFFEATRLRARAGD
                     EMEEKQKQVTASETRLNQISSEINGIQEAISQANNKRSTAVSRIHDAEDNLKTAQTNLL
                     NSQIKDAVDATVSFYQTLSEKYGEKYSKMAQELADKSKGKKISNVNEALAAFEKYKDVL
                     NKKFSKADRDAIFNALEAVKYEDWAKHLDQFAKYLKITGHVSFGYDVVSDILKIKDTGD
                     WKPLFLTLEKKAVDAGVSYVVVLLFSVLAGTTLGIWGIAIVTGILCAFIDKNKLNTINE
                     VLGI"
                     /name="colicin-like pore-forming protein"
     gene            complement(4026..4367)
                     /locus_tag="WCU01_RS25480"
                     /old_locus_tag="WCU01_25480"
     CDS             complement(4026..4367)
                     /locus_tag="WCU01_RS25480"
                     /old_locus_tag="WCU01_25480"
                     /inference="COORDINATES: protein motif:HMM:NF015489.4"
                     /GO_function="GO:0015643 - toxic substance binding
                     [Evidence IEA]"
                     /GO_process="GO:0030153 - bacteriocin immunity [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin E1 family microcin immunity protein"
                     /protein_id="WP_000058755.1"
                     /translation="MSLRYYIKNILFGLYCALIYIYLITKNNEGYYFLASDKMLYAIVI
                     STILCPYSKYAIEHIFFKFIKKDFFRKRKNLNNAPVAKLNLFMLYNLLCLVLAIPFGLL
                     GLFISIKNN"
                     /name="colicin E1 family microcin immunity protein"
     gene            4415..4552
                     /locus_tag="WCU01_RS25485"
                     /old_locus_tag="WCU01_25485"
     CDS             4415..4552
                     /locus_tag="WCU01_RS25485"
                     /old_locus_tag="WCU01_25485"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001405930.1"
                     /GO_component="GO:0019867 - outer membrane [Evidence IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin release lysis protein"
                     /protein_id="WP_001329514.1"
                     /translation="MRKRFFVGIFAINLLVGCQANYIRDVQGGTVAPSSSSKLTGISVQ
                     "
                     /name="colicin release lysis protein"
     Typing          471..710
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="7.6e-123"
     Typing          complement(43..212)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.186"
                     /coverage="89.0"
                     /evalue="7.259999999999999e-67"
     Typing          complement(4799..5153)
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.91"
                     /coverage="82.0"
                     /evalue="3.76e-168"
     Typing          720..1039
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="3.11e-62"
ORIGIN
        1 atggaaaaac gcctgcggcg ctggcttctt ccggtgcttt gctttttgct cacatgttct
       61 ttccggcttt atcccctgat tctgtggata accgtattac cgcttttgag tgagctgaca
      121 ccgctcgccg cagtcgaacg tccgagcgta gcgagtcagt gagcgaggaa gcggaagagc
      181 gccttatgtg acattttctc cttacgctct gttgtgccgt tcggcatcct gtcctgagcg
      241 ttatctctct gtgctatttt ctacttcaaa gcgtgtctgg atgctgttct ggagttcttc
      301 tgcgagttcg tgcagcttct cacacatggt agcctgttcg tcagcatcga gtgcgtccag
      361 cttttcgagc agcgtcaggc tttggctttt tatgaatcct gccatgttga gtacggcttg
      421 ctgctgcttg ttcatctttt cgttttctcc gttctgtctg tcatctgcgt tgtgtgatta
      481 tatcgcgtac cacttttcga ctgttttacc gccggtattc tgccgtctga cgctttgacg
      541 ggtatttctg cctgacaata ctgtcactgc caaaaaactg ccgtgccttt gtcggtaatt
      601 cgaacttgct gacaggacag gatgtgtaat tgttataccg cgcatacatg cacgctatta
      661 caattaccct ggtcagggct ttgccccgac acccatgtca gatacggagc catgttttat
      721 gacaaaacga agtggaagta atacgcgcag gcgggctatc agtcgccctg ttcgtctgac
      781 ggcagaagaa gaccaggaaa tcagaaaaag ggctgctgaa tgcggcaaga ccgtttccgg
      841 ttttttacgg gcggcagctc tcggtaagaa agttaactca ctgactgatg atcgggtact
      901 gaaagaagtt atgagactgg gggcgttaca gaaaaaactc tttatcgacg gcaagcgtgt
      961 cggggacagg gagtatgcgg aggtgctgat cgctattacg gagtatcacc gtgccctgtt
     1021 atccaggctt atggcagatt agcttcccgg agagaaaact gtcgaaaact gacggtatga
     1081 acaccgtaag ctcccaaagt gatcaccatt cgctttcatg catagctatg cagagagctg
     1141 aaaacgatcc tgacgcatcc ttcctgtttt tccggggtaa aacatctctt tttgcggtgt
     1201 ctgcgtcaga atcgcgttca gcgcgtttca gtggtgcgta caattaaggg attatggtaa
     1261 atccacttac tgtctgccct cgtagccatc gagataaacc gcagaaatcg tgtcagccag
     1321 cagcctggat tttttcgggg taaggtcttt gctgcggtaa tcagtacccg caaattgagt
     1381 tgtgccccgg agtgagttta aaaattcctg gctgtgaaac tgttgaatgc gttgttgcac
     1441 atcactccgt gattttcctg tcgctttatc tttagctccc atatcccaga actgccgaaa
     1501 aaaaggcacc atcattcgtg ttgtgtcggc tttttgggtg gaaaagttgg gatcaaaacc
     1561 gtcatcagaa gcatatacgt aatgccgggt atgttgttcc acgctgccct ttggggtaca
     1621 ggctgtgaga gctactgttg ctgttatcat ggcgataaga caaagtttgt ttccggtacg
     1681 tctcatgagt gtctccctac cttaaagtat ttattctcgg tgagttatta tccgaagatt
     1741 atcttatcat cagtttctga gcgcgttcag tgaccgaaca gcctggacca gaatccccgt
     1801 ttcttttcct gctccagagc ctgcctgagc tgggctatct cattctgtag ctgtttccgt
     1861 tctgcttcct ggcgccggcg ctccgtatcc tgggcttgtt tatcctcaag catcagcgtc
     1921 aggcattgtt tcagctcatt cagttcccgg agaatgcgtt ctgtctgctg atcatgaggt
     1981 ttttctgagt gtccttgagt gtgcctttct ggtgtctcat tccgctttaa ttcgccgtat
     2041 gcccggatca gttcactggt ttcaaactcc cgtcgtccgt cctggctggt acggtaactg
     2101 acaagacctg agcgcatatc acggtaaaac tgtgaacgcg atcttccagt cattttcagt
     2161 gcgtcccgga gtgtgtgcca tgccataaag ttacagtgtc ccataggtgt ctcatctcat
     2221 ggtttcagta aaacataatg aggtctgaga acggtaatgt ttgtgctggt ttttgtggca
     2281 tcgggtggaa atagcacgtg gtgtgggtgg ctgttttttt gatcgttttc acaaaaatga
     2341 aaatccacag ggttgacagg gaaaatgcag cggcgtaatt ttaaactgta tataaaacca
     2401 gtgattatat atacagtata ttgcttttaa ctatttgttt ttaatgtcaa agaggatttt
     2461 ataatggaaa cagctgtagc gtactataaa gatggtgttc cttatgatga taaggggcag
     2521 gtaatcatta ctcttttgaa tggtaatcca gacgggagtg gctctggcgg tggtggtgga
     2581 actggaggta gcaaaagtga aagttctgca gccattcatg ccacagctaa atggtctact
     2641 gctcaattga agaaaacgca ggcagaacag gctgcccgag caaaagctgc cgcagaagca
     2701 caggctaaag caaaagcaaa ccgggatgcg ctgactcaac atctgaagga tattgtgaat
     2761 gaggcgcttc gccataattc cactcatccg gaggttattg acctggctca tgccaataat
     2821 gcagcgatgc aggcagaagc agagcggttg cgccttgcaa aagcagaaga aaaagcccgt
     2881 aaagaagcgg aagctgcgga aaaggctttt caggaagcag aacaacgacg taaagagata
     2941 gagaaggagc aggctgaaac agaacgccaa ttgaaactgg ctgaggatga agagaaacgc
     3001 ctggcagcat tgagtgaaga ggcccgggct gtggaggtgg cacaaaaaaa tcttgctgct
     3061 gcacaatctg agctggcgaa agtggatgaa gagattaata cgctcaatac ccgtttaagc
     3121 tccagtattc atgcccgtga tgcagaaacg aatacgctgt ccggaaaacg aaatgagttg
     3181 gatcaggcat ctgctaaata taaagaactg gatgaaaggg ttaaactttt atctcctagg
     3241 gcgaatgatc cgcttcagag tcgtcctttt tttgaggcca ccagactacg ggcgagagct
     3301 ggtgatgaga tggaggaaaa acaaaagcag gtaacagcat cagaaacgcg tcttaaccag
     3361 attagctctg agataaatgg aatccaagag gctatttctc aggctaataa taagcgaagt
     3421 acagcagttt cacgtattca tgatgctgaa gataatttga aaacagcaca gactaatctc
     3481 ctgaactcgc agattaagga tgctgtggat gcaacagtta gcttttatca aacgctatct
     3541 gaaaaatatg gtgaaaaata ttcaaaaatg gcacaggaac ttgctgataa atctaaaggt
     3601 aagaaaatca gcaatgtgaa tgaagctcta gctgcttttg agaaatacaa ggatgtatta
     3661 aataagaaat tcagcaaagc agaccgtgat gcaattttca atgcactgga ggcggttaag
     3721 tatgaagact gggctaagca tttagatcag tttgccaagt acttgaagat tacgggacat
     3781 gtttcttttg gatatgatgt ggtatctgat atcctaaaaa ttaaggatac aggtgactgg
     3841 aagccgctat ttcttacatt agagaagaaa gctgtagatg ctggagttag ttatgttgtt
     3901 gttttacttt ttagtgtgct tgctggaact acattaggta tctgggggat tgctattgtt
     3961 acaggcattc tatgtgcctt tattgataag aataaactta atactataaa tgaggtgttg
     4021 ggtatttaat tattctttat tgatataaac agtcctagca atccaaatgg gattgctagg
     4081 accaaacaaa gtagattgta tagcataaat aggtttaatt ttgccacggg ggcattattt
     4141 aggttttttc tttttctgaa aaaatctttc tttatgaact taaaaaatat gtgttcaata
     4201 gcatattttg aatatgggca tagaatagtg cttatcacta ttgcgtatag catcttatct
     4261 gacgctagga aataataccc ttcgttgttt tttgttataa ggtatatata tataagtgcg
     4321 cagtataggc caaacaaaat attttttatg tagtatctta aactcataaa ttaaacctcg
     4381 ttatatattc ttttcatttt ataaggatcg agttatgagg aaaagatttt ttgtgggaat
     4441 attcgctata aacctccttg ttggatgtca ggctaactat atacgtgatg ttcagggagg
     4501 gactgtggct ccatcatctt cttctaaatt gacggggatc tctgttcagt agaaaagatc
     4561 aaaggatctt cttgagatcc tttttttctg cgcgtaatct gctgcctgta aacgaaaaaa
     4621 ccgcctgggg aggcggtttg atcgaaggtt aagtcagttg gggaactgct taaccgaggt
     4681 aactggcttc agcagagcgc agataccaaa tactgtcctt ccagtgtagc cgtagtcggg
     4741 ccactacttc aagaactctg ttgcaccatt tgcgccatca tcgctctgct aaccaagtta
     4801 ccaacggctg ctgccagtgg cgctaagtcg tgtcttaccg ggttggactc aagacgatag
     4861 ttaccggata aggcgcagcg gtcgggctga acggggggtt cgtgcacaca gcccagcttg
     4921 gagcgaacga cctacaccga gccgagatac caacagcgtg agctatgaga aagcgccacg
     4981 cttcccgaag ggagaaaggc ggacaggtat ccggtaagcg gcagggtcgg aacaggagag
     5041 cgcacgaggg agcttccagg gggaaacgcc tggtatcttt atagtcctgt cgggtttcgc
     5101 cacctctggc ttgagcgtcg atttttgtga tgctcgtcag gggggcggag cct
//
