LOCUS       NZ_CP035756             5681 bp    DNA     circular CON 20-JUN-2024
DEFINITION  Escherichia coli E110019 plasmid pE110019_5, complete sequence.
ACCESSION   NZ_CP035756
VERSION     NZ_CP035756.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN02435896
            Assembly: GCF_000167875.2
KEYWORDS    RefSeq.
SOURCE      Escherichia coli E110019
  ORGANISM  Escherichia coli E110019
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5681)
  AUTHORS   Hazen,T.H., Vyas,G., Parankush,S., Tallon,L. and Rasko,D.A.
  TITLE     Complete genome assembly of atypical Enteropathogenic Escherichia
            coli isolate E110019
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5681)
  AUTHORS   Hazen,T.H., Vyas,G., Parankush,S., Tallon,L. and Rasko,D.A.
  TITLE     Direct Submission
  JOURNAL   Submitted (06-FEB-2019) Institute for Genome Sciences, University of
            Maryland, School of Medicine, 670 W. Baltimore St., Baltimore, MD
            21201, USA
REFERENCE   3  (bases 1 to 5681)
  AUTHORS   Rasko,D., Rosovitz,M., Myers,G., Seshadri,R., Cer,R., Jiang,L.,
            Ravel,J., Fricke,W.F. and Sebastian,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (16-JUN-2008) J. Craig Venter Institute, 9704 Medical
            Center Drive, Rockville, MD 20850, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: JUN-2018
            Assembly Method                   :: HGAP v. 3
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 15.6x
            Sequencing Technology             :: PacBio RSII
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_000167875.2-RS_2024_06_20
            Annotation Date                   :: 06/20/2024 03:03:26
            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)                     :: 5,468
            CDSs (total)                      :: 5,348
            Genes (coding)                    :: 5,054
            CDSs (with protein)               :: 5,054
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 294
            CDSs (without protein)            :: 294
            Pseudo Genes (ambiguous residues) :: 0 of 294
            Pseudo Genes (frameshifted)       :: 129 of 294
            Pseudo Genes (incomplete)         :: 149 of 294
            Pseudo Genes (internal stop)      :: 61 of 294
            Pseudo Genes (multiple problems)  :: 41 of 294
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP035756.1.
            Bacteria and source DNA available from Dr. David Rasko, University
            of Maryland Baltimore, Institute for Genome Sciences, 670 W.
            Baltimore St., Baltimore, MD 21201.
            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..5681
                     /organism="Escherichia coli E110019"
                     /mol_type="genomic DNA"
                     /strain="E110019"
                     /serovar="O111:H9"
                     /db_xref="taxon:340186"
                     /plasmid="pE110019_5"
     misc_feature    complement(339..455)
                     /inference="COORDINATES: nucleotide
                     motif:Rfam:14.4:RF01497"
                     /inference="COORDINATES: profile:INFERNAL:1.1.5"
                     /note="AL1L pseudoknot; Derived by automated computational
                     analysis using gene prediction method: cmsearch."
                     /db_xref="RFAM:RF01497"
     gene            complement(410..736)
                     /locus_tag="ECE110019_RS27860"
     CDS             complement(410..736)
                     /locus_tag="ECE110019_RS27860"
                     /inference="COORDINATES: protein motif:HMM:NF013677.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS3 family transposase"
                     /protein_id="WP_000165261.1"
                     /translation="MTKNTRFSPEVRQRAVRMVLESQGEYDSQWATICSIAPKIGCTPE
                     TLRVWVRQHERDTGGGDGGLTTAERQRLKELERENRELRRSNDILRQASAYFAKAEFDR
                     LWKK"
                     /name="IS3 family transposase"
     gene            922..1781
                     /gene="blaTEM"
                     /locus_tag="ECE110019_RS27020"
                     /pseudo=""
     CDS             922..1781
                     /gene="blaTEM"
                     /locus_tag="ECE110019_RS27020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_032489893.1"
                     /GO_function="GO:0008800 - beta-lactamase activity
                     [Evidence IEA]"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="TEM family class A beta-lactamase"
                     /name="blaTEM"
     gene            complement(1920..2069)
                     /locus_tag="ECE110019_RS27025"
     CDS             complement(1920..2069)
                     /locus_tag="ECE110019_RS27025"
                     /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_001677812.1"
                     /translation="MNKQQQAVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EEGV"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2354..2677
                     /gene="mobA"
                     /locus_tag="ECE110019_RS27030"
     CDS             2354..2677
                     /gene="mobA"
                     /locus_tag="ECE110019_RS27030"
                     /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(2912..3267)
                     /gene="lsoB"
                     /locus_tag="ECE110019_RS27035"
                     /pseudo=""
     CDS             complement(2912..3267)
                     /gene="lsoB"
                     /locus_tag="ECE110019_RS27035"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052605.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system antitoxin LsoB"
                     /name="lsoB"
     gene            complement(3287..4325)
                     /gene="lsoA"
                     /locus_tag="ECE110019_RS27040"
                     /pseudo=""
     CDS             complement(3287..4325)
                     /gene="lsoA"
                     /locus_tag="ECE110019_RS27040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052606.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system mRNA
                     endoribonuclease LsoA"
                     /name="lsoA"
     gene            complement(5199..5645)
                     /locus_tag="ECE110019_RS27865"
     CDS             complement(5199..5645)
                     /locus_tag="ECE110019_RS27865"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="IS3 family transposase"
                     /protein_id="WP_001438717.1"
                     /translation="MAFIIDVFAGYIVGWRVSPSMETTFVLDALEQALWARRPSGTVHH
                     SDKGSQYVSLAYTQRLKEAGLLASTGSTGDSYDNAMAESINGLYKAEVIHRKSWKNRAE
                     VELATLTWVDWYNNRRLLERLGHTPPAEAEKAYYASIGNDDLAA"
                     /name="IS3 family transposase"
     ARG             923..1392
                     /name="TEM-93"
                     /gene="TEM-93"
                     /gene_name="TEM beta-lactamase"
                     /tool="rgi"
                     /drug_class="monobactam; cephalosporin; penam; penem"
                     /identity="100.0"
                     /coverage="54.55"
     ARG             1459..1781
                     /name="TEM-185"
                     /gene="TEM-185"
                     /gene_name="TEM beta-lactamase"
                     /tool="rgi"
                     /drug_class="monobactam; cephalosporin; penam; penem"
                     /identity="100.0"
                     /coverage="37.41"
     Typing          2105..2345
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.12e-123"
     Typing          complement(4630..5158)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.61"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          2355..2674
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="2.18e-62"
     Typing          complement(5203..5681)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="87.5"
                     /coverage="100.0"
                     /evalue="1.03e-87"
ORIGIN
        1 agtaaatcag ccacccacag ctggtcaggt cgttctgcca cgaactgacg gtttacgcgg
       61 tcgcctgcgg caacggcttt ccggctgatg gtcgtacgga cctttttacc ccggagaaca
      121 ccggcaagtc ccataaccgc catgagacgt gccacagtgc atctggccac tctgatacct
      181 tcccgtaaca actgacgcca gactttacgc acaccgtata ccttgtgatt ttcatcgtat
      241 acgcgctgta tctctttctt cagccagtca tcgcgctgcg cacgggcact gcgtttatcc
      301 ggatgatgtc gctgttgctg acagtggtaa tacgttgacg gggcaatatg cagttcgctg
      361 catagcggtc cgaccccgta ctgctcacgc agcttatcca gcagtggcat cattttttcc
      421 agaggcggtc gaactccgcc ttcgcaaaat aagcggaagc ctggcgaagg atatcgttac
      481 tgcggcgcag ttcacgattt tcacgctcca gctctttcag acgctgacgt tcagcggtgg
      541 tgagccctcc atcaccgccc ccggtatccc gctcatgctg gcgaacccag acacgcagag
      601 tctccggcgt acagccaatc tttggagcaa tggaacaaat tgtcgcccat tgtgagtcat
      661 attcgccctg actttccaga accatacgga ctgcccgttg acggacttca ggggaaaaac
      721 gagtattttt agtcatcctg tttacctctt tctcaggaag tttagtctcc aggattcccg
      781 gggcggttca caggtggcac ttttcgggga aatgtgcgcg gaacccctat ttgtttattt
      841 ttctaaatac attcaaatat gtatccgctc atgagacaat aaccctggta aatgcttcaa
      901 taatattgaa aaaggaagag tatgagtatt caacattttc gtgtcgccct tattcccttt
      961 tttgcggcat tttgccttcc tgtttttgct cacccagaaa cgctggtgaa agtaaaagat
     1021 gctgaagatc agttgggtgc acgagtgggt tacatcgaac tggatctcaa cagcggtaag
     1081 atccttgaga gttttcgccc cgaagaacgt tttccaatga tgagcacttt taaagttctg
     1141 ctatgtggtg cggtattatc ccgtgttgac gccgggcaag agcaactcgg tcgccgcata
     1201 cactattctc agaatgactt ggttgagtac tcaccagtca cagaaaagca tcttacggat
     1261 ggcatgacag taagagaatt atgcagtgct gccataacca tgagtgataa cactgctgcc
     1321 aacttacttc tgacaacgat cggaggaccg aaggagctaa ccgctttttt gcacaacatg
     1381 gggatcatgt aactcgcctt gatcgttggg aaccggagct gaatgaagcc ataccaaacg
     1441 acgagcgtga caccacgatg cctgcagcaa tggcaacaac gttgcgcaaa ctattaactg
     1501 gcgaactact tactctagct tcccggcaac aattaataga ctggatggag gcggataaag
     1561 ttgcaggacc acttctgcgc tcggcccttc cggctggctg gtttattgct gataaatctg
     1621 gagccggtga gcgtgggtct cgcggtatca ttgcagcact ggggccagat ggtaagccct
     1681 cccgtatcgt agttatctac acgacgggga gtcaggcaac tatggatgaa cgaaatagac
     1741 agatcgctga gataggtgcc tcactgatta agcattggta actgtcagac caagtttact
     1801 catatatact ttagattgat ttaaaacttc atttttaatt taaaaggatc taggtgaaga
     1861 tcctttttga taatctcatg accaaaatcc cttaacgtga gttttcgttc cactgagcgt
     1921 cagacccctt cttctgcgag ttcgtgcagc ttctcacaca tggcagcctg ttcgtcagca
     1981 tcgagtgcgt ccagcttttc gagcagcgtc aggctctggc tttttatgaa tcctgccatg
     2041 ttgagtacag cttgctgctg cttgttcatc ttttcgtttt ctccgttctg tctgtcatct
     2101 gcgttgtgtg attatatcgc gtaccacttt tcgactgttt taccgccggt attctgccgt
     2161 ctgacgcttt gacgggtatt tctgcctgac aatactgtca ctgccaaaaa actgccgtgc
     2221 ctttgtcggt aattcgagct tgctgacagg acaggatgtg caattgttat accgcgcata
     2281 catgcacgct attacaatta ccctggtcag ggcttcgccc cgacacccca tgtcagatac
     2341 ggagccatgt tttatgacaa aacgaagtgg aagtaatacg cgcaggcggg ctatcagtcg
     2401 ccctgttcgt ctgacggcag aagaagacca ggaaatcaga aaaagggctg ctgaatgcgg
     2461 caagaccgtt tctggttttt tacgggcggc agctctcggt aagaaagtta actcactgac
     2521 tgatgaccgg gtgctgaaag aagttatgcg actgggggcg ttgcagaaaa aactctttat
     2581 cgacggcaag cgtgtcgggg acagagagta tgcggaggtg ctgatcgcta ttacggagta
     2641 tcaccgtgcc ctgttatcca ggcttatggc agattaactt cccggagaga aactgtcgaa
     2701 aacagacggt atgaacgccg taagccccca aaccgatcgc cattcacttt catgcatagc
     2761 tatgcagtga gctgaaagcg atcctgacgc atttttccgg tttaccccgg ggaaaacatc
     2821 tctttttgcg gtgtctgcgt cagaatcgcg ttcagcgcgt tttggcggtg cgcgtaatga
     2881 gacgttatgg taaatgtctt ctggcttgat attatattgg aatgcctttt ttcaaagcaa
     2941 atgatgtggc ttggatagaa ggtttacgtt gatcttatca aagttttttt taaagaacga
     3001 agccgagagc tcagataaat cattatattc atcagttttc gtaactttgt ttaatgtgta
     3061 acttgaaaac ttctcgccat taaatgacgt atagacgtaa cgatcttttt ttccaccgtt
     3121 aggaattatt aaatcaaaaa aaacatcacc cttgcttttc tttttcttca agtcggattc
     3181 gatttttgag aaaaattcgc tcgggctata aatatcagta gcatagacaa taaataaagt
     3241 tttatcttta ttttttattg cttctatttg atatttttta tctttttcat aatttcaacc
     3301 tagctacgcc accatctatt aattggcaaa cggtatcgat gattgcgatt gattctaatt
     3361 tgttaattgt cttcgtgtca gctattcctg gtttcatatg aaacaaacca tgcctgttct
     3421 catgccagta agtgtagcat tcacacaaaa cttccgctat ttcaccattt atagtttctt
     3481 ggtgtatttc tctgattata tatttgggtt tgttttcagt gaagtattcg ccaaggttct
     3541 ttgatgatga tggattgcaa acatcattaa gtatttgata tataaagcct tctatggctc
     3601 ttaatgcaga gaagcagtat gttgagtaat cttccatttc gacatctatt tttttcatta
     3661 ttagcgagca tgatagctgt tttttgatat cttcatggat tttatcgatg cttttggtag
     3721 tttgctatgc aactcggact caatagtttc ttttttatgt caacattaaa ttctttattt
     3781 ttttgttcga caatctcttt catgtttagt attgagcaca tgaaatcgtt aatcaaactc
     3841 gcgatttgaa ggtattttcc ttggaattga atagagccgc gcttgtaaat ttttgccctg
     3901 accctgtcac cattgctggt ggtcataata tattggtgtt tacaattagg atcgttatta
     3961 ttatcttctg ttattgttat cccctcttca gaaagaaatt caaatagatt tgccctgtca
     4021 tcatcactga attttggaat ggtgtattca aagttctttg tgtctgaata caaacagttt
     4081 tcttttataa tcaaggcgat ttcatcaaag taagtgttat tttgcccaga cgctcttccg
     4141 atagtggtat ttccgcctga tggcattagt tttattaaga agtctattcc tttatatgtg
     4201 ccagatatgt gagtttctct ttcgtttttt acattagagg aatagtttgt gacgccattc
     4261 tgcgtcagag cagactcaat cttgtcaata ttgatattta gtgctttaaa cgggttctgt
     4321 gccattgggt caatccgttg tttttttgaa tatgtacaga tcttgttttt tgtcaacgga
     4381 atagctgttc gttgacttga tagaccgatt gattcatcat ctcataaata aagaaaaacc
     4441 accgctacca acggtggttt tctcaaggtt cgctgagcta ccaactcttt gaaccaaggt
     4501 aactggcttg gaggagcgca gtcaccaaaa tctgttcttt cagtttagcc ttaacaggtg
     4561 cataacttca agacaaactc ctctaaatca gttaccaatg gctgctgcca gtggcgataa
     4621 gtcgtgtctt accgggttgg actcaagacg atagttaccg gataaggcgc agcggtcggg
     4681 ctgaacgggg gttcgtgcac acagcccagc ttggagcgaa cgacctacac cgaactgaga
     4741 taccaacagc gtgagctatg agaaagcgcc acgcttcccg aagggagaaa ggcggacagg
     4801 tatccggtaa gcggcagggt cggaacagga gagcgcacga gggagcttcc agggggaaac
     4861 gcctggtatc tttatagtcc tgtcgggttt cgccacctct ggcttgagcg tcgatttttg
     4921 tgatgctcgt cagggggcgg agcctatgga aaaacgcctg cggcgttggc ttcttccggt
     4981 gctttgcttt ttgctcacat gttctttccg gctttatccc ctgattctgt ggataaccgt
     5041 attaccgctt ttgagtgagc tgacaccgct cgccgcagtc gaacgaccga gcgtagcgag
     5101 tcagtgagcg aggaagcgga agagcgcctt atgtgacatt ttctccttac gctctgtgaa
     5161 ccgccccggg tttcctggag agtgttttat ctgtgaactc aggctgccag atcatcgttt
     5221 ccgatggaag cataataagc tttttctgct tctgccggag gagtatggcc cagcctttcc
     5281 agcaatcgtc gattgttata ccagtccacc cacgtgagtg tggccagttc cacttctgca
     5341 cggtttttcc agctcttacg gtgtattacc tccgctttgt aaagaccatt gatgctctcc
     5401 gccatcgcgt tgtcatacga gtcgcctgta cttcctgttg atgccagtaa tccggcttcc
     5461 ttaagccgct gtgtgtaggc cagcgataca tactgagaac ctttatcact gtgatggacc
     5521 gtgccggacg gtcgacgggc ccataacgcc tgctccagtg catccagcac gaatgtcgtc
     5581 tccatggacg gtgagacccg ccaccccaca atgtatccgg caaacacatc aatgatgaac
     5641 gccacataga cgaagccctg ccatgtgctg acgtaagtaa a
//
