LOCUS       NZ_CP101304             5686 bp    DNA     circular CON 27-JUL-2023
DEFINITION  Escherichia coli strain 2000-3039 plasmid pO45-2, complete sequence.
ACCESSION   NZ_CP101304
VERSION     NZ_CP101304.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN24907327
            Assembly: GCF_024300705.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5686)
  AUTHORS   Kalalah,A. and Eppinger,M.
  TITLE     Whole genome sequencing, comparative phylogenetic analysis, and
            phenotypic profiling of the non-O157 Big Six Shiga toxin-producing
            Escherichia coli strains obtained from ATCC
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5686)
  AUTHORS   Kalalah,A. and Eppinger,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-JUL-2022) Molecular Microbiology and Immunology, The
            University of Texas at San Antonio, One UTSA Circle, San Antonio, TX
            78249, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: JUN-2022
            Assembly Method :: Unicycler v. Galaxy Version 0.4.8.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 246x
            Sequencing Technology :: Oxford Nanopore MiniION; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/27/2023 05:20:46
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,626
            CDSs (total)                      :: 5,501
            Genes (coding)                    :: 5,212
            CDSs (with protein)               :: 5,212
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 95
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 289
            CDSs (without protein)            :: 289
            Pseudo Genes (ambiguous residues) :: 0 of 289
            Pseudo Genes (frameshifted)       :: 106 of 289
            Pseudo Genes (incomplete)         :: 163 of 289
            Pseudo Genes (internal stop)      :: 65 of 289
            Pseudo Genes (multiple problems)  :: 43 of 289
            Pseudo Genes (short protein)      :: 4 of 289
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP101304.1.
            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..5686
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="2000-3039"
                     /serotype="O45:H2"
                     /host="Homo sapiens"
                     /culture_collection="ATCC:BAA-2193"
                     /db_xref="taxon:562"
                     /plasmid="pO45-2"
                     /collection_date="2021"
                     /note="ATCC lot#70014570"
     gene            complement(383..1450)
                     /locus_tag="NMK59_RS28015"
                     /old_locus_tag="NMK59_28015"
     CDS             complement(383..1450)
                     /locus_tag="NMK59_RS28015"
                     /old_locus_tag="NMK59_28015"
                     /EC_number="3.1.21.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001009472.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="CfrBI family restriction endonuclease"
                     /protein_id="WP_001009472.1"
                     /translation="MNFKDKNCFPNELIALAKISKNDVLDKFGTDVFKKVVYDVLTGKN
                     VREFTEILTRTRLLESNLSFFDFFVDKMKEGITPKQLYLYAKNALSNKSYVKSNQPVLE
                     WMVMMTNKQTQNVLRDEHGDGFDRLALRTQEEILKIKNGYEDKIGEISIGGQKVSLEDF
                     CYIILSLGSQTLTIRGSEKSLHGKYFEKLILGSLFTIMGFEYKEKIEEGLNAKCFTLST
                     RADDRESDATLVFNGKAIRVDIGFIGRGNTEISLDKVSRFRRMDDIGGVMHNISTMVIV
                     DVIGDRSRIVNMAEEIDGKVVAMSDPYWVAKVSSYISSKLNVDDLLEDKPQLKDIQSFI
                     SDALENVDLEKYIKL"
                     /name="CfrBI family restriction endonuclease"
     gene            1527..2657
                     /locus_tag="NMK59_RS28020"
                     /old_locus_tag="NMK59_28020"
     CDS             1527..2657
                     /locus_tag="NMK59_RS28020"
                     /old_locus_tag="NMK59_28020"
                     /EC_number="2.1.1.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000216732.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0008170 - N-methyltransferase activity [Evidence IEA]"
                     /GO_process="GO:0009307 - DNA restriction-modification
                     system [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="site-specific DNA-methyltransferase"
                     /protein_id="WP_000216732.1"
                     /translation="MTVKNNYLNRGYLVTSTTQAKKIAKLHLEKLDLADKFSFGLPEVD
                     DRYHVWRVPLVATGHRIGEIVINSKTSTIDYKKSSKSPFLIKKAMEVVHTPKKVKKEKK
                     IISKSPLNNMLLQGNCAETLKKLPDESVNLVFTSPPYYNAKPEYSEYHTYDEYLSLLRS
                     VIKECHRVLSEGRFFVINVSPVLIRRASRNEASKRIAVPFDLHRLFIEEGYEFIDDIHW
                     VKPEGAGWALGRGRRFAADRNPLQYKPVPVTEYILVYRKKTDKLIDWNIRNHHSKEDVF
                     DSKIGDDYEKTNLWKINPSRNRKHPATFPYGLAERVIKYYSFKNDVILDPFAGSGTTAK
                     AAIDLGRRFVMCEISKQYIDLIIEGTMLGGDLKIIN"
                     /name="site-specific DNA-methyltransferase"
     gene            complement(3041..3274)
                     /locus_tag="NMK59_RS28025"
                     /old_locus_tag="NMK59_28025"
     CDS             complement(3041..3274)
                     /locus_tag="NMK59_RS28025"
                     /old_locus_tag="NMK59_28025"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137445.1"
                     /translation="MTELETHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(3281..3799)
                     /locus_tag="NMK59_RS28030"
                     /old_locus_tag="NMK59_28030"
     CDS             complement(3281..3799)
                     /locus_tag="NMK59_RS28030"
                     /old_locus_tag="NMK59_28030"
                     /function="essential for mobilization of the plasmid"
                     /inference="COORDINATES: protein motif:HMM:NF016710.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_031942530.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNNEFRRLGESVSEAVTSNE
                     TKIRDAIALFTASTEKSLEKHREGVKEAMMQHRKDVLKLAGNTGMMLLGIVFLLFTASG
                     GTLWYLGGRIQANLEEIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVIPFQ
                     GKEWVHLKE"
                     /name="MbeB family mobilization protein"
     gene            complement(<3837..4268)
                     /locus_tag="NMK59_RS28035"
                     /old_locus_tag="NMK59_28035"
                     /pseudo=""
     CDS             complement(<3837..4268)
                     /locus_tag="NMK59_RS28035"
                     /old_locus_tag="NMK59_28035"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(4477..4800)
                     /locus_tag="NMK59_RS28040"
                     /old_locus_tag="NMK59_28040"
     CDS             complement(4477..4800)
                     /locus_tag="NMK59_RS28040"
                     /old_locus_tag="NMK59_28040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_000956000.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGTR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            4865..5056
                     /locus_tag="NMK59_RS28045"
                     /old_locus_tag="NMK59_28045"
     CDS             4865..5056
                     /locus_tag="NMK59_RS28045"
                     /old_locus_tag="NMK59_28045"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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_000165974.1"
                     /translation="MTKQEKTALNMARFIRGQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(5208..5522)
                     /locus_tag="NMK59_RS28050"
                     /old_locus_tag="NMK59_28050"
     CDS             complement(5208..5522)
                     /locus_tag="NMK59_RS28050"
                     /old_locus_tag="NMK59_28050"
                     /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_224157910.1"
                     /translation="MSVDFCDARQGGGAYGKNASGAAFFALCLFAHMFFPALSPDSVDN
                     RIAVFEQADSARRSRTTERSESVSEEAEKRLDVHFLLTHLCGISHPAWCTFHTMRPDAE
                     "
                     /name="hypothetical protein"
     Typing          complement(5142..5221)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.67e-34"
     Typing          2..149
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.987"
                     /coverage="95.0"
                     /evalue="2.02e-66"
     Typing          5253..5686
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.379"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(2938..4487)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.183"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ctcggctcgg tgtaggtcgt tcgctccaag ctgggctgtg tgcacgaacc ccccgttcag
       61 cccgaccgct gcgccttatc cggtaactat cgtcttgagt ccaacccgga aagacacgta
      121 aaaacgccac tggcagcagc cattggtaac cgggttagca gagcgagatt tataagttgg
      181 taacagagtt cttgaagtat cagcctgatt ctggctacac tagaagaaca agttttggtg
      241 gtctgcgctc tgcttaagcc agattacctg gttagataat ctgccaggat tagctaacct
      301 ttgaaaaacc acctgccagg gtggtttttc tttatgtaga gattatgctt ttaataagca
      361 cgcagtcaag gattacaatc tcttataatt taatgtattt ttccagatct acattctcta
      421 atgcatcaga tataaaagac tgtatgtctt taagttgagg tttatcctct aaaagatcat
      481 ctacattcag tttcgaacta atataggaag agacctttgc aacccaatac ggatcactca
      541 tcgcaacaac tttaccatca atctcttcag ccatattaac tattctactt ctatcaccaa
      601 taacgtcaac aataaccatt gtgcttatat tatgcatcac tccgccaata tcatccattc
      661 gtctaaatct agatacttta tccaaactta tttctgtgtt acccctacca ataaaaccaa
      721 tgtcaaccct aatcgccttc ccattaaaaa caagagtagc atcagactcc ctgtcatcag
      781 ctcttgttga aagagtaaaa catttagcat ttaacccttc ttcaattttt tctttatatt
      841 caaaacccat tattgtaaat aaagaaccga gtattagctt ttcaaaatat ttaccatgaa
      901 gagatttctc agatccccta atagttaaag tttgcgaacc aagagataaa ataatatagc
      961 aaaaatcttc taaagacacc ttttgcccac caatagatat ctctccaatt ttatcttcat
     1021 acccgttttt tattttaagt atttcttctt gcgtccttaa agcaagtcta tcaaaaccat
     1081 ccccatgctc atctcttaaa acattttggg tctgtttatt tgtcatcata accatccact
     1141 cgagaacagg ttgattagac ttaacataag acttgttcga taatgcattt tttgcataga
     1201 gataaagctg ctttggcgtt atcccttctt tcattttatc cacaaaaaag tcaaaaaaag
     1261 agagattgct ttctaacaat ctagtacgag ttagtatttc agtgaattcg cgaacatttt
     1321 tacctgttaa aacatcataa acaacctttt taaaaacatc cgttccgaac ttatctaaaa
     1381 catcattttt tgaaattttc gccaacgcta tgagttcgtt agggaaacaa tttttatcct
     1441 tgaaattcat atcctcacca tggacatagt aaaaatgaga tgctaagata gcaggttgta
     1501 tggtaacaga tcgatagtta ggaaaaatga cagttaaaaa caattactta aacagaggtt
     1561 atttggtaac ctctacgact caggcgaaaa aaatagcaaa gttgcaccta gagaaattag
     1621 acttagctga taaattttcc tttgggttac ctgaagtcga tgatcggtac catgtatggc
     1681 gtgtaccatt agtagcgaca ggccacagga ttggtgaaat agttataaat tcaaaaacgt
     1741 caactattga ttataagaaa agttcgaagt ctccatttct tattaagaaa gcaatggagg
     1801 ttgtccatac cccaaaaaag gtaaaaaaag aaaaaaaaat catatcaaag tcaccattaa
     1861 ataacatgtt actacaaggc aactgcgcgg agaccttgaa aaaattacct gatgaatcag
     1921 tgaacttagt attcacatca ccgccatatt acaatgccaa accagagtat tccgaatatc
     1981 atacatatga tgaatacctc tctctattgc gttcagtaat aaaagagtgc catagagttt
     2041 taagcgaagg tcgttttttc gtcatcaatg tctcgcccgt tttaataaga agggcgtcac
     2101 ggaatgaagc atcaaaaaga atagctgttc cttttgactt gcacaggtta tttatagaag
     2161 aaggctatga attcatagat gatatacatt gggttaaacc agaaggagct ggctgggctt
     2221 taggtagagg ccgtcgattc gcagctgacc gcaatccgtt gcaatataaa ccagtaccag
     2281 taactgagta cattcttgtt tacagaaaaa aaactgataa attaatagat tggaacataa
     2341 gaaaccatca tagcaaagag gatgtttttg actcaaaaat cggcgacgat tacgaaaaga
     2401 caaacctatg gaaaataaat ccatctcgta acagaaaaca tcctgctaca tttccatacg
     2461 gtctggcaga aagagttata aaatactatt ctttcaaaaa tgatgttatt ttagatcctt
     2521 ttgctggatc gggaacaaca gcaaaagcag caattgattt aggcagaaga tttgtgatgt
     2581 gtgagatatc aaagcagtat attgatctga tcatagaagg aaccatgcta ggtggtgatt
     2641 taaaaatcat aaattaatca aactttactg tggtaaaagc cgccttaagg cggcttattt
     2701 acgcgtcaac atcagccaca ttgtcgaatt taccataatc ccttaattgt acgcaccgcc
     2761 aaaacgcgtt cagcgcgatc acagcagcag acaggtaaaa atggcaacaa accccccgaa
     2821 aaactgccgc aatcgcgcct gataaatttt aaccgcatga atacctatgc aaccagatgg
     2881 tacagaccac attagcctgt cttaatccac ttaacctgcc atttttcatg gtttcaccat
     2941 cccagcgaag ggccatccag cgtgcgttcc tgtatttccg gctgacgctc ccgttccagg
     3001 gataacacat gttcgcgctc ctgtatcagc cgttcctctc ttatctccag ttctcgctgt
     3061 ataactggct caagcgttct gtctgctcgc tcaagtgctg cacctgctga ctcaactgca
     3121 tgacccgctc gttcagcatc gcgttgtccc gttgcgtaag cgaaaacatc ttctgcaatt
     3181 ccacgaaggc gctctcccat tcgctcagcc gctgcatata gtcctgttgc agctgctcta
     3241 aggcgttcag caaatgtgtt tccagctctg tcactctgtg tcactccttc agatgtaccc
     3301 actctttccc ctgaaaggga atcacctccg ctgatttccc gtacggaagg acaaggaatt
     3361 tcctgttccc gtcctgcaca aactccacgc cccatgtctt cgcgttcagt ttctgcaatg
     3421 tctcttcctg cttcctgatt tcttccaggt tcgcctgtat cctccctcca agataccaga
     3481 gcgtcccgcc actcgctgta aacaggagaa agactatccc cagtaacatc atgcccgtat
     3541 tccctgccag ctttaacacg tccttcctgt gctgcatcat cgcctctttc accccttccc
     3601 ggtgtttttc cagcgatttc tctgtcgagg ctgtgaacag ggctatagcg tctctgattt
     3661 tcgtctcgtt tgaggtcaca gcctcgctga cagactcgcc gagcctcctg aactcgttgt
     3721 tcagcatttt ctctgtagat tcggctctct ctttcagctt tttctcgaac tccgcgcccg
     3781 tctgtaaaag attgctcata aaatgctcct ttcagcttga tattcctccc gccgttcggg
     3841 tctgcaatgc tgatactgct tcgcgtcacc ctgaccactt caatccctgc ctccgtgagc
     3901 gcctgaatca catcctgacg gccttttatc tccccgacat gataaagagc gtctatcccg
     3961 cgtgtgacgc tctctgcaag cgcctgtttc gtttccggca ggttatcagg aagggtcagc
     4021 gtccggcggt tctccggggc gttcgggtca tgcagcccgt aatggtgatt caccagcgtc
     4081 tgccaggcat caattctcgg cctgtctgcc cggtcgtagt acggctgtag gcgttttccg
     4141 gtctccagct ccatgttcgg aatgacaaaa ttcagctcaa gccgtccctt gtcctggtgc
     4201 tccacccaca ggatgctgta ctgatttttt tcgagaccgg gcatcagtac acgctcaaag
     4261 ctcgccatca ctttttcacg tcctcccggc ggcagctcct tctccgcgaa cgacagaaca
     4321 cctgacgtgt atttcttcgc aaatggcgtg gcatcgatga gttcccggac ttcttccgga
     4381 ttaccctgaa gcaccgttgc cccttcccgg ttacgctccc ttcccagcag gtaatcaacc
     4441 ggaccactgc caccaccttt tcccctggca tgaaatttaa ctatcatccc gcgtcccctg
     4501 ttccctgacg gccagacgca gccggcgcag ctcatccccg atggccatca gtgcggccac
     4561 tacctgaacc cggtcaccgg aagaccactg tccgctgttc accttcctcg ctgtctgatt
     4621 caggttattc ccgatggcgg ccagctgacg cagtaacggc ggagccagtg tcggcagctt
     4681 cccggaacgg gcaaccggct cacccaggca gacccgccgc atccataccg ccagttgttt
     4741 accctcacag cgttccagta accgggcatg ttcatcatca gtaacccgta tcgtgagcat
     4801 cctctcgcgt ttcatcggta tcattacccc catgaacaga aatccccctt acacggaggc
     4861 atcagtgact aaacaggaaa aaaccgccct taacatggcc cgtttcatca gaggccagac
     4921 attaacgctg ctggagaaac ttaacgaact ggacgcagat gaacaggcag atatctgtga
     4981 atcgcttcac gaccacgccg atgagcttta ccgcagctgc ctcgcacgtt tcggggatga
     5041 cggtgaaaac ctctgacaca tgcagctccc ggaaacggtc acagcttgtc tgtgagcgga
     5101 tgccgggagc cgacaagccc gtcaggacgc gtcagcgggt tttagcgggt gtcggggcgc
     5161 agccctgacc cagtcacgta gcgatagcgg agtgtatact ggcttactta ttcggcatca
     5221 gggcgcattg tatgaaaagt gcaccatgcc gggtgtgaaa tgccgcacag atgcgtaagg
     5281 agaaaatgca cgtccaggcg cttttccgct tcctcgctca ctgactcgct gcgctcggtc
     5341 gttcgactgc ggcgagcgga gtctgcttgc tcaaaaacag caatacggtt atccacagaa
     5401 tcaggagata aggccggaaa gaacatgtga gcaaaaagac aaagggcaaa aaaagccgcg
     5461 ccgctggcgt tttttccata ggctccgccc ccctgacgag catcacaaaa atcgacgctc
     5521 aagtcagagg tggcgaaacc cgacaggact ataaagatac caggcgtttc cccctggaag
     5581 ctccctcgtg cgctctcctg ttccgaccct gccgcttacc ggatacctct ccgcctttct
     5641 cccttcggga agcgtggcgc tttctcatag ctcacgctgt tggtat
//
