LOCUS       NZ_CP095516             6466 bp    DNA     linear   CON 20-JAN-2024
DEFINITION  Escherichia coli strain GN02323 plasmid p2323-3.
ACCESSION   NZ_CP095516
VERSION     NZ_CP095516.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN27361457
            Assembly: GCF_026651145.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6466)
  AUTHORS   Bethke,J.H., Ma,H.R., Tsoi,R., Cheng,L., Xiao,M. and You,L.
  TITLE     Vertical and horizontal gene transfer tradeoffs direct plasmid
            fitness
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6466)
  AUTHORS   Bethke,J.H., Ma,H.R., Tsoi,R., Cheng,L., Xiao,M. and You,L.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-APR-2022) Molecular Genetics and Microbiology, Duke
            University, CIEMAS Building 101 Science Drive, Durham, NC 27705, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. 6.0.0.47841
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 488x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/20/2024 05:01:55
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,091
            CDSs (total)                      :: 4,979
            Genes (coding)                    :: 4,728
            CDSs (with protein)               :: 4,728
            Genes (RNA)                       :: 112
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 251
            CDSs (without protein)            :: 251
            Pseudo Genes (ambiguous residues) :: 0 of 251
            Pseudo Genes (frameshifted)       :: 107 of 251
            Pseudo Genes (incomplete)         :: 154 of 251
            Pseudo Genes (internal stop)      :: 53 of 251
            Pseudo Genes (multiple problems)  :: 56 of 251
            Pseudo Genes (short protein)      :: 4 of 251
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP095516.1.
            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/
FEATURES             Location/Qualifiers
     source          1..6466
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="GN02323"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p2323-3"
                     /geo_loc_name="USA"
                     /lat_lon="36 N 78.9 W"
                     /collection_date="2004"
                     /collected_by="Vance G. Fowler Jr."
                     /genotype="73"
     gene            401..1111
                     /locus_tag="MW403_RS24855"
                     /old_locus_tag="MW403_24880"
     CDS             401..1111
                     /locus_tag="MW403_RS24855"
                     /old_locus_tag="MW403_24880"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000967646.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000967645.1"
                     /translation="MLYWKKMPSLWIGNRIAEFSDLDTAKAIAALKIYLTFCLFCKESD
                     SGHRTVELTFSNLCEIASLSRSLVNEGLKILYAKELIKNISPTARKKIYTVDVLENHND
                     GWCKLPFKGVVDEDKKISAFQSMHNRYPFELLALQTYMYLLYARDNNSDYTLARKKTIC
                     KKLKCKLPELNKAITYLIHIGLLDRVVKKSIENIPLEMFHDSYYFYIKTGSKSALTYRR
                     KSEPPVIPEADLPF"
                     /name="hypothetical protein"
     gene            1905..2099
                     /locus_tag="MW403_RS24860"
                     /old_locus_tag="MW403_24885"
     CDS             1905..2099
                     /locus_tag="MW403_RS24860"
                     /old_locus_tag="MW403_24885"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_001041636.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADVQAAMCERLHELA
                     EELQNSIQVHFEAENETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(2336..4015)
                     /locus_tag="MW403_RS24865"
                     /old_locus_tag="MW403_24890"
     CDS             complement(2336..4015)
                     /locus_tag="MW403_RS24865"
                     /old_locus_tag="MW403_24890"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000598747.1"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA];
                     GO:0016887 - ATP hydrolysis activity [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="AAA family ATPase"
                     /protein_id="WP_001774712.1"
                     /translation="MIKVQLPTREHRLHELNLNYGDVVFFIGQNGSGKSSLLNNLFQKI
                     GSQSSVYVLAHRKNTFSSDIIDFSNSEYKNAQGWIFNEIKGSQCRYRVNYDSQMVAIPI
                     VKLKNKVIARALSFVDSFKSNNNQPAELIKSEVDVLNMVFADAKLSIEFFLDDEANVMA
                     RNIKGENPDVYPISMLSDGEKSALIIASEIICADENTTIFLDEPERHMHRSIVSPLLSS
                     LMKYRRDCVFFVATHELSLPAFFDNVKVVNVKNCYFSEQREPIYWDFNVVEDYDELFNG
                     VDEQTKIDILGARDKVLFVEGVTSSLDRDLYSAIFPMVSVVSKQKCDLVELAVKGLRLN
                     DEIHRVSAFGIIDNDNKVQAKVDNLKKDFIFSLDVHSIESIYYHPRMIKFVIDFVKEAN
                     GIDNVDALFMEIHDFAIDAINEKRDHLCCRAVEKTIRADLMSAIPKQQDIKNRIKFNKE
                     IDIECYVNKEIAAFDAMIAERNLDALVSRYPIRETNLLAHVAKKCGFADRSRYELNVIR
                     TIKSNADARAFVLSLLGGLDEAILGCSDTENSPADTHTVFAM"
                     /name="AAA family ATPase"
     gene            complement(4012..>4602)
                     /locus_tag="MW403_RS24870"
                     /old_locus_tag="MW403_24895"
                     /pseudo=""
     CDS             complement(4012..>4602)
                     /locus_tag="MW403_RS24870"
                     /old_locus_tag="MW403_24895"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001697689.1"
                     /note="internal stop; incomplete; partial in the middle of
                     a contig; missing N-terminus; 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            5166..5297
                     /locus_tag="MW403_RS25515"
     CDS             5166..5297
                     /locus_tag="MW403_RS25515"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001422066.1"
                     /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_071525238.1"
                     /translation="MHDPPVQSDRCALSGNYHLESNPERHDLSPLAAAIGKGCTRDY"
                     /name="replication initiation protein"
     gene            5938..6453
                     /locus_tag="MW403_RS24875"
                     /old_locus_tag="MW403_24900"
     CDS             5938..6453
                     /locus_tag="MW403_RS24875"
                     /old_locus_tag="MW403_24900"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000675351.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type III toxin-antitoxin system ToxN/AbiQ family
                     toxin"
                     /protein_id="WP_000675351.1"
                     /translation="MKFYTISSRYIEYLKGFEDKVPNSEDPNYQNPKAFIGIVLEIQGH
                     KYLAPLTSPKPWHSTIKESSPSFFKLHENGVPENQLGLINLKFMIPIIEAEVSLLDLNG
                     MPNTAYKRMLYKQLQFIRVNSDKIAEKSELLRKLVLQGKMQGTCNFSLLEEKYRDFGKE
                     ANDTEEGE"
                     /name="type III toxin-antitoxin system ToxN/AbiQ family
                     toxin"
     Typing          complement(1390..1645)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="94.574"
                     /coverage="89.0"
                     /evalue="2.65e-108"
     Typing          complement(1770..1869)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.02"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          4762..5334
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.828"
                     /coverage="90.0"
                     /evalue="5.34e-173"
ORIGIN
        1 tcctgaatag tgtccgaaac cgagtgatct tggacactat tcaggtctaa tattcaaaac
       61 tcaacggttc gactcacata catagttcac ggtgaaccat attatgatta atacaaatac
      121 caaaactcaa ataaaaaacc gttaaaaaca acaagataaa aaattaacat cacttttatc
      181 tttctagata gatttttttg aaggcgttac aacgccttca caccctgaga taataaaaac
      241 aacaagaagc gattacgagg ggtgaaaaat gtttgagaaa ggcgtgtgtc tggttgagag
      301 acttgcgaaa gtcgcagcgg taataactaa ccttgtgctc tcactttcta tattgggatt
      361 ggtctatttc atctttcaaa acttggcctt gaggtgattc atgctgtact ggaaaaaaat
      421 gccttcacta tggataggaa ataggatcgc tgaattcagc gatcttgata cagcaaaagc
      481 tatagcggca ttaaaaattt atttaacatt ctgcctgttt tgcaaagagt cagactctgg
      541 ccacagaacg gttgagttaa cctttagcaa cctttgcgag atagcgtcat taagccgttc
      601 cttggtgaac gaaggcctta aaattcttta tgcaaaagag ctgataaaaa acatatcgcc
      661 gactgcacga aaaaagattt ataccgtgga tgtgctagaa aatcataatg atggatggtg
      721 caagcttcca tttaaaggag ttgtcgacga ggacaaaaaa ataagtgcat ttcaatccat
      781 gcacaacaga tatccctttg agttactagc cttacaaact tacatgtatc ttctttacgc
      841 tcgtgataat aacagcgact acacactggc taggaaaaag accatatgca aaaaattgaa
      901 atgcaaatta cctgaactaa acaaagcaat cacctacctt atccatatag gtttgcttga
      961 tagagttgtg aaaaaatcca tagaaaacat acctctagag atgtttcatg actcgtacta
     1021 tttctatata aaaacaggca gtaagagcgc tctaacctac agaaggaaat cagaaccgcc
     1081 agttattcca gaagccgact taccattttg attgtttatt ccacaccaat tatcacacgg
     1141 attgaacata acatccgttg cccgcacctc agaaacgcgc tgaacgcgat tctgacgcaa
     1201 ataccgcaaa aagagatgtt ttccccaagg taaaccgaaa aaatgcgtca ggatcgtttt
     1261 cagctcgctg catagctatg catgaaagtg aatggcgaac ggtttgggcg catacggtgc
     1321 ccatgagaca cattttcgga cattttcagt tcgtgaatcc ctgactcatt gctacatatc
     1381 tgaacagaca cccctagcag cgcccccagg ggcatcctgt aaaaaaacac accgcgccgc
     1441 tagcagcacc cctaatataa aatgatgttt tttatgaaaa tagtcagtac cacccctaca
     1501 aagcggtgtc ggcgcggtgt tgtagccgcg ccgacaccgc ttttttaaat atcacaaaga
     1561 gagcaagaga aactaatttg tcataactct ctatttataa agaaaaatca gcaaaaaatt
     1621 gtttttgcgt ggggtgtggg catttcaggc atgagaacag actcgcgttt ttccggagta
     1681 tcagcggaat tattgattaa gaaacactcg acgcagagcg aaattttatg caacagcggc
     1741 tgcactgcac agggattatt tatcagttga tatgctgtgc catgatacgt cctaaaaaaa
     1801 acaggacagg atgtgcaatt gtaataccgt cgcccgcaac gtcttacaat taccacctag
     1861 tcagggtcca cccgacaccc ggtactgacg gagaacaacg gaaggtgaac aaacagcaac
     1921 aaactgcgct gaatatggcg cgatttatca aaagccagag cctgacactg cttgaaaaac
     1981 tggatgctct ggatgccgac gtacaggcgg ccatgtgtga acgactgcac gaactcgcag
     2041 aagaactcca gaacagcatc caggttcact ttgaggccga aaatgaaaca ggaacataac
     2101 gaagctgacg aaggcggtca cggcttgccc gtgagcattt tcgtcagcag acaagcccgt
     2161 cagggcgcgt cagcgggttt taacgggtgt cggggcgcag ccctgaccca gccacgtagc
     2221 gatagcggag tgtatactga cttaatacag caactatcgt acatcgcggt caagtcacgc
     2281 acaaacaaaa agccccgcaa aagcagggct gttatctgat ataggttgtt tagtctcaca
     2341 tagcaaaaac tgtatgggta tcagctgggc tattttccgt atctgaacat cccaaaatag
     2401 cttcatctaa ccctccgagg agggataaaa caaatgctct agcgtcagca ttactcttga
     2461 tcgtacgaat cacgtttaac tcatatctag agcgatcggc aaaaccacat tttttagcta
     2521 catgtgccaa caaatttgtt tctcggatag ggtagcgtga gactaacgca tccaaatttc
     2581 gttccgcgat cattgcatca aatgcagcaa tttctttatt aacataacat tcaatatcaa
     2641 tttctttatt aaacttaatg cggttcttaa tatcttgctg ttttggtatg gccgacatta
     2701 agtctgccct tattgttttt tcaactgcac ggcagcataa gtgatcgcgc ttttcattta
     2761 tggcatcaat agcgaagtca tgaatttcca taaataaggc atcaacatta tctatcccat
     2821 tagcctcttt tacaaagtca atgacaaact taatcattct aggatgataa taaatcgact
     2881 caatagaatg aacgtcgaga ctaaaaatga agtctttctt taagttatcg accttcgcct
     2941 gcaccttgtt atcattatca atgataccaa acgccgatac tcgatgaatt tcgtcattta
     3001 gtctcaagcc ttttaccgcc aattcaacca aatcacattt ttgtttagat acaactgaaa
     3061 ccataggaaa tatggccgaa tataaatcac ggtcaaggct agacgtaaca ccttcaacaa
     3121 atagaacctt atccctagcg ccaagtatat ctattttagt ttgctcatca acaccattga
     3181 ataattcgtc ataatcctca acaacattga aatcccagta tatcggttct ctttgttcgg
     3241 aaaaatagca gtttttaacg ttaaccactt tcacgttatc aaaaaacgca ggcaagctta
     3301 actcgtgggt ggcaacaaaa aaaacacaat ctctacgata tttcattaaa gatgaaagca
     3361 gcggagacac aatgcttctg tgcatatgtc gctcaggctc atctaagaaa atagttgtgt
     3421 tttcatcagc gcaaataatc tcactggcaa taattagtgc acttttttca ccgtcagaaa
     3481 gcattgatat aggataaaca tcaggatttt cacctttaat attccttgcc ataacgttgg
     3541 cttcatcatc tagaaagaac tcaatagata atttggcatc agcaaaaacc atgtttagaa
     3601 catcaacctc tgactttatt aactctgccg gctgattgtt atttgattta aatgaatcta
     3661 cgaaacttaa agccctggct atcactttgt tttttaattt tactataggt atggcaacca
     3721 tctgtgagtc ataattaact ctgtatctac attgactgcc tttaatttca ttaaaaatcc
     3781 atccctgcgc atttttatac tcactattac tgaaatcaat aatgtcgctg ctgaatgtat
     3841 tttttctatg cgctaaaaca tatactgatg attgagatcc tattttttga aaaagattat
     3901 ttaataggct ggatttacca ctaccattct gaccaataaa aaaaacgaca tcgccataat
     3961 taagattaag ctcatgaaga cgatgttctc tagtaggtaa ctgaactttt atcattttcc
     4021 tttctcttta gcttttaatc taaaatacgt tgaacgacta attcctaaat taatccatgg
     4081 agagtttaat gaaggcctac ctcctccttt actttttttc ccacatagag attagatgtc
     4141 tgccgaatgg gtctttttta taaaatcatc aaatgatgac tctgtaaaat ttttattagt
     4201 ccacttagct acacttttgg caatacccat gacttcgttc tcgtctaaag gtgcggagaa
     4261 ctgcaggttg taggctttag cgcgttcaaa gcaagcttgt agccattggt catactgcgg
     4321 ccagccttgg tggatagcgc ggtaagccca cttgcgggtt ttatcgaaga gggtgcagtt
     4381 acggcctaaa ccgtagtccg gtaggatttc gcggtcatta gctgcgccaa ggtcgaggta
     4441 gtcggctaat cagtcgaggg tgtagagctc aggctgccaa acggtgatct gccagtgcag
     4501 gtggttcgga ttctcgcaaa ttagccctga ataccccgca tcggcgccca attgtttacg
     4561 cagcgcattc tcaatgacgg ctgcatattt gaggggggcg gcaagccccc tgaaccagtc
     4621 acagaaggca cctcgcagag gggacgctgt gagtactgac ttaactatgc ggtatcagtg
     4681 cggattgtat gaaaagtgcg ctattgacgg tgtgaaatgc cgcacagatg cgtaaggaga
     4741 aaatgcaaat gcctacgctc ttccgcttcc tcgctcacta actcgctgcg ctcggtcgtt
     4801 cggctgcggc gagcggtatc agctcactca gagacggtaa tacggttatc cacagaatca
     4861 ggggataagg ccggaaagaa catgtgagca aaaaggcaaa gccagggcaa aaggccgcgc
     4921 cgctggcgtt tttccatagg ctccgccccc ctgacaagca tcacagaatc tgacgctcaa
     4981 atcagtggtg gcgaaacccg acaggactta aagataccag gcgtttcccc ctggtggctc
     5041 cctcgtgcgc tctcctgttc ctgcctttcg gtttaccggt gtcattccgc tgttatggcc
     5101 gcgtttatct cattccacgc ctgacactcg gttccgggta ggcagttcgc tccaagctgg
     5161 actgtatgca cgaccccccc gttcagtccg accgctgcgc cttgtccggt aactatcatc
     5221 ttgagtccaa cccggaaaga cacgacttat cgccactggc tgcggccatt ggtaaggggt
     5281 gtacaagaga ttactgatgc agagttcttg aagttagaac caaactacgg ctaaactgga
     5341 aggacgaatt tggtggcagc ggtcttgtac accctgttac cacggttcag aagttcccca
     5401 acttactgaa ccatcgaaaa accacctccc caggtggttt tttcgttttc agagcaagag
     5461 attacgcgta gaaaaaaagg atctcaagca gatccttttt gattcatgtc ataacccaac
     5521 ttaccccccc ccacactgaa ctgatgaaaa aaacagtcaa ctctggaatc agtactttaa
     5581 aaaagcctca aatgacattt tgaggggata cagcggcaag ggctacaact acacagctgc
     5641 aagttaccta gttgtaagcc taggcgaaga tcaggtatac tcgaatcaag gtgatttgct
     5701 acctttaagt gcagctagaa attcaggtga tttgctacct ttaagtgcag ctagaaattc
     5761 aggtgatttg ctaccttaag tgcagctaga aattcaggtg atttgctacc tttaagtgca
     5821 gctagaaatt caggtgattt gctaccttaa gtgcagctag aaatttaggt catttactac
     5881 cttaaagtaa tacagtaaaa gaggcgacta cacagtcgcc ttttttacga gaaaaaaatg
     5941 aaattttaca ctatatcaag cagatacatt gaatacctaa agggattcga agacaaagtt
     6001 cccaatagcg aagatcctaa ctatcagaat ccgaaagctt tcattggcat tgtgttagag
     6061 attcaagggc ataagtatct agccccttta acatccccaa agccatggca tagcactatt
     6121 aaagaatcat cgcctagctt ctttaagctc catgaaaatg gtgtccccga aaatcagctc
     6181 ggattgatta atctgaagtt catgattcca atcatcgaag ccgaagtatc cttacttgac
     6241 ttgaacggta tgccgaatac cgcctacaag agaatgctct ataagcagct ccagtttatt
     6301 cgtgtaaatt cagacaaaat agctgagaaa tcagagcttt taaggaagct cgtcctgcaa
     6361 ggaaaaatgc aaggaacatg taatttttcc ctgttagaag aaaaataccg agatttcggc
     6421 aaagaagcta atgacacgga agaaggcgag taacgcttca ttgcca
//
