LOCUS       NZ_CP111096             3306 bp    DNA     circular CON 06-JAN-2024
DEFINITION  Escherichia coli strain TW14588 plasmid pTW14588-2, complete
            sequence.
ACCESSION   NZ_CP111096
VERSION     NZ_CP111096.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31023066
            Assembly: GCF_033970745.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3306)
  AUTHORS   Peroutka-Bigus,N., Nielsen,D., Trachsel,J., Kudva,I. and Loving,C.
  TITLE     Phenotypic connections with genomic virulence signatures in Shiga
            toxin producing O157 Escherichia coli
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3306)
  AUTHORS   Nielsen,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-SEP-2022) FSEPRU, USDA-ARS, 1920 Dayton Ave, Ames, IA
            50010, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Flye v. 2.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 541x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/06/2024 11:31:10
            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)                     :: 5,642
            CDSs (total)                      :: 5,510
            Genes (coding)                    :: 5,214
            CDSs (with protein)               :: 5,214
            Genes (RNA)                       :: 132
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 102
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 296
            CDSs (without protein)            :: 296
            Pseudo Genes (ambiguous residues) :: 0 of 296
            Pseudo Genes (frameshifted)       :: 104 of 296
            Pseudo Genes (incomplete)         :: 170 of 296
            Pseudo Genes (internal stop)      :: 72 of 296
            Pseudo Genes (multiple problems)  :: 41 of 296
            Pseudo Genes (short protein)      :: 4 of 296
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP111096.1.
            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..3306
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="TW14588"
                     /isolation_source="Lettuce"
                     /host="Lactuca sativa"
                     /db_xref="taxon:562"
                     /plasmid="pTW14588-2"
                     /geo_loc_name="USA"
                     /lat_lon="42.0308 N 93.6319 W"
                     /collection_date="2006"
     gene            complement(join(3302..3306,1..1036))
                     /gene="lsoA"
                     /locus_tag="ORM94_RS27685"
                     /old_locus_tag="ORM94_27575"
     CDS             complement(join(3302..3306,1..1036))
                     /gene="lsoA"
                     /locus_tag="ORM94_RS27685"
                     /old_locus_tag="ORM94_27575"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052606.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system mRNA
                     endoribonuclease LsoA"
                     /protein_id="WP_000068433.1"
                     /translation="MAQNPFKALNINIDKIESALTQNGVTNYSSNVKNERETHISGTYK
                     GIDFLIKLMPSGGNTTIGRASGQNNTYFDEIALIIKENCLYSDTKNFEYTIPKFSDDDR
                     ANLFEFLSEEGITITEDNNNDPNCKHQYIMTTSNGDRVRAKIYKRGSIQFQGKYLQIAS
                     LINDFMCSILNMKEIVEQKNKEFNVDIKKETIESELHSKLPKSIDKIHEDIKKQLSCSL
                     IMKKIDVEMEDYSTYCFSALRAIEGFIYQILNDVCNPSSSKNLGEYFTENKPKYIIREI
                     HQETINGEIAEVLCECYTYWHENRHGLFHMKPGIADTKTINKLESIAIIDTVCQLIDGG
                     VARLKL"
                     /name="lsoA"
     gene            complement(1301..1414)
                     /locus_tag="ORM94_RS27690"
                     /old_locus_tag="ORM94_27580"
     CDS             complement(1301..1414)
                     /locus_tag="ORM94_RS27690"
                     /old_locus_tag="ORM94_27580"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001459398.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLSPLAAAIGN"
                     /name="hypothetical protein"
     gene            1525..1773
                     /locus_tag="ORM94_RS27695"
                     /old_locus_tag="ORM94_27585"
     CDS             1525..1773
                     /locus_tag="ORM94_RS27695"
                     /old_locus_tag="ORM94_27585"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000919062.1"
                     /translation="MAGSEQESARGSFRGETPGIFIVLSGFATSGLSVDFCDARQGGGA
                     YGKTPAVLASSGALLFAHMFFPALSPDSVDNRITAFE"
                     /name="hypothetical protein"
     gene            complement(1901..2095)
                     /locus_tag="ORM94_RS27700"
                     /old_locus_tag="ORM94_27590"
     CDS             complement(1901..2095)
                     /locus_tag="ORM94_RS27700"
                     /old_locus_tag="ORM94_27590"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /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_001041624.1"
                     /translation="MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA
                     EELQNSIQTRFEVENSTEI"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2367..2690
                     /gene="mobA"
                     /locus_tag="ORM94_RS27705"
                     /old_locus_tag="ORM94_27595"
     CDS             2367..2690
                     /gene="mobA"
                     /locus_tag="ORM94_RS27705"
                     /old_locus_tag="ORM94_27595"
                     /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(2925..3305)
                     /gene="lsoB"
                     /locus_tag="ORM94_RS27710"
                     /old_locus_tag="ORM94_27600"
     CDS             complement(2925..3305)
                     /gene="lsoB"
                     /locus_tag="ORM94_RS27710"
                     /old_locus_tag="ORM94_27600"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052605.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system antitoxin LsoB"
                     /protein_id="WP_000710826.1"
                     /translation="MKKDKKYQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKK
                     SKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNF
                     DKINVNLLSKATSFALKKGIPI"
                     /name="lsoB"
     Typing          2133..2358
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="89.583"
                     /coverage="99.0"
                     /evalue="1.05e-76"
     Typing          complement(1343..1872)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.413"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          2368..2687
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="4.0199999999999997e-60"
ORIGIN
        1 atttcaacct agctacgcca ccatctatta attggcaaac ggtatcgatg attgcgattg
       61 attctaattt gttaattgtc ttcgtgtcag ctattcctgg tttcatatga aacaaaccat
      121 gcctgttctc atgccagtaa gtgtagcatt cacacaaaac ttccgctatt tcaccattta
      181 tagtttcttg gtgtatttct ctgattatat atttgggttt gttttcagtg aagtattcgc
      241 caaggttctt tgatgatgat ggattgcaaa catcattaag tatttgatat ataaagcctt
      301 ctatggctct taatgcagag aagcagtatg ttgagtaatc ttccatttcg acatctattt
      361 ttttcattat tagcgagcat gatagctgtt ttttgatatc ttcatggatt ttatcgatgc
      421 tttttggtag tttgctatgc aactcggact caatagtttc tttttttatg tcaacattaa
      481 attctttatt tttttgttcg acaatctctt tcatgtttag tattgagcac atgaaatcgt
      541 taatcaaact cgcgatttga aggtattttc cttggaattg aatagagccg cgcttgtaaa
      601 tttttgccct gaccctgtca ccattgctgg tggtcataat atattggtgt ttacaattag
      661 gatcgttatt attatcttct gttattgtta tcccctcttc agaaagaaat tcaaatagat
      721 ttgccctgtc atcatcactg aattttggaa tggtgtattc aaagttcttt gtgtctgaat
      781 acaaacagtt ttcttttata atcaaggcga tttcatcaaa gtaagtgtta ttttgcccag
      841 acgctcttcc gatagtggta tttccgcctg atggcattag ttttattaag aagtctattc
      901 ctttatatgt gccagatatg tgagtttctc tttcgttttt tacattagag gaatagtttg
      961 tgacgccatt ctgcgtcaga gcagactcaa tcttgtcaat attgatattt agtgctttaa
     1021 acgggttctg tgccattggg tcaatccgtt gttttttttg aatatgtaca gatcttgttt
     1081 ttttgtcaac ggaatagctg ttcgttgact tgatagaccg attgattcat catctcataa
     1141 ataaagaaaa accaccgcta ccaacggtgg ttttctcaag gttcgctgag ctaccaactc
     1201 tttgaaccaa ggtaactggc ttggaggagc gcagtcacca aaatctgttc tttcagttta
     1261 gccttaacag gtgcataact tcaagacaaa ctcctctaaa tcagttacca atggctgctg
     1321 ccagtggcga taagtcgtgt cttaccgggt tggactcaag acgatagtta ccggataagg
     1381 cgcagcggtc gggctgaacg gggggttcgt gcacacagcc cagcttggag cgaacgacct
     1441 acaccgaact gagataccaa cagcgtgagc tatgagaaag cgccacgctt cccgaaggga
     1501 gaaaggcgga caggtatccg gtaagtggca gggtcggaac aggagagcgc acgagggagc
     1561 ttccgggggg aaacgcctgg tatctttata gtcctgtcgg gtttcgccac ctctggcttg
     1621 agcgtcgatt tttgtgatgc tcgtcagggg ggcggagcct atggaaaaac gcctgcggtg
     1681 ctggcttctt ccggtgcttt gctttttgct cacatgttct ttccggcttt atcccctgat
     1741 tctgtggata accgtattac cgcctttgag tgagctgaca ccgctcgccg cagtcgaacg
     1801 accgagcgta gcgagtcagt gagcgaggaa gcggaagagc gccttatgtg acattttctc
     1861 cttacgctct gttgtgccgt tcggcatcct gccctgagcg ttatatctct gtgctatttt
     1921 ctacttcaaa gcgtgtctgt atgctgttct ggagttcttc tgcgagttcg tgcagcttct
     1981 cacacatggt ggcctgctcg tcagcatcga gtgcgtccag tttttcgagc agcgtcaggc
     2041 tctggctttt tatgaatccc gccatgttga gtgcagtttg ctgctgcttg ttcatctttc
     2101 tgttttctcc gttctgtctg tcatctgcgt cgtgtgatta tatcgcgcac cacttttcga
     2161 ccgtcttacc gccggtattc tgccgacgga catttcagtc agacaacact gtcactgcca
     2221 aaaaacagca gtgctttgtt ggtaattcga acttgcagac aggacaggat gtgcaattgt
     2281 tataccgcgc atacatgcac gctattacaa ttaccctggt cagggcttcg ccccgacacc
     2341 ccatgtcaga tacggagcca tgttttatga caaaacgaag tggaagtaat acgcgcaggc
     2401 gggctatcag tcgccctgtt cgtctgacgg cagaagaaga ccaggaaatc agaaaaaggg
     2461 ctgctgaatg cggcaagacc gtttctggtt ttttacgggc ggcagctctc ggtaagaaag
     2521 ttaactcact gactgatgac cgggtgctga aagaagttat gcgactgggg gcgttgcaga
     2581 aaaaactctt tatcgacggc aagcgtgtcg gggacagaga gtatgcggag gtgctgatcg
     2641 ctattacgga gtatcaccgt gccctgttat ccaggcttat ggcagattag cttcccggag
     2701 agaaactgtc gaaaacagac ggtatgaacg ccgtaagccc ccaaaccgat cgccattcac
     2761 tttcatgcat agctatgcag tgagctgaaa gcgatcctga cgcatttttc cggtttaccc
     2821 cggggaaaac atctcttttt gcggtgtctg cgtcagaatc gcgttcagcg cgttttggcg
     2881 gtgcgcgtaa tgagacgtta tggtaaatgt cttctggctt gatattatat tggaatgcct
     2941 tttttcaaag caaatgatgt ggctttggat agaaggttta cgttgatctt atcaaagttt
     3001 tttttaaaga acgaagccga gagctcagat aaatcattat attcatcagt tttcgtaact
     3061 ttgtttaatg tgtaacttga aaacttctcg ccattaaatg acgtatagac gtaacgatct
     3121 ttttttccac cgttaggaat tattaaatca aaaaaaacat cacccttgct tttctttttc
     3181 ttcaagtcgg attcgatttt tgagaaaaat tcgctcgggc tataaatatc agtagcatag
     3241 acaataaata aagttttatc tttatttttt attgcttcta tttgatattt tttatctttt
     3301 ttcata
//
