LOCUS       NZ_CP039838             3371 bp    DNA     circular CON 14-NOV-2023
DEFINITION  Escherichia coli O55:H7 strain USDA5905 plasmid pUSDA5905_6,
            complete sequence.
ACCESSION   NZ_CP039838
VERSION     NZ_CP039838.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11229503
            Assembly: GCF_013343615.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli O55:H7
  ORGANISM  Escherichia coli O55:H7
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3371)
  AUTHORS   Bono,J.L.
  TITLE     Comparison of 54 complete closed STEC O157:H7 genomes
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3371)
  AUTHORS   Bono,J.L.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-APR-2019) Meat Safety and Quality Research Unit,
            United State Department of Agriculture, State Spur 18D, P.O. Box
            166, Clay Center, NE 68933, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. 3.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 299.0x
            Sequencing Technology             :: PacBio RSII
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/14/2023 02:24:46
            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)                     :: 5,597
            CDSs (total)                      :: 5,462
            Genes (coding)                    :: 5,177
            CDSs (with protein)               :: 5,177
            Genes (RNA)                       :: 135
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 106
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 285
            CDSs (without protein)            :: 285
            Pseudo Genes (ambiguous residues) :: 0 of 285
            Pseudo Genes (frameshifted)       :: 117 of 285
            Pseudo Genes (incomplete)         :: 153 of 285
            Pseudo Genes (internal stop)      :: 77 of 285
            Pseudo Genes (multiple problems)  :: 55 of 285
            Pseudo Genes (short protein)      :: 4 of 285
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP039838.1.
            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..3371
                     /organism="Escherichia coli O55:H7"
                     /mol_type="genomic DNA"
                     /strain="USDA5905"
                     /serotype="O55:H7"
                     /isolation_source="Food (meat)"
                     /db_xref="taxon:244320"
                     /plasmid="pUSDA5905_6"
                     /collection_date="1994"
     gene            complement(1130..1363)
                     /locus_tag="E3175_RS26500"
                     /old_locus_tag="E3175_27130"
     CDS             complement(1130..1363)
                     /locus_tag="E3175_RS26500"
                     /old_locus_tag="E3175_27130"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137389.1"
                     /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_000137389.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHEVTQRNNA
                     ILNERVVILSQQVQRLAGQVDRLSRLFIANNS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1370..1930)
                     /locus_tag="E3175_RS26505"
                     /old_locus_tag="E3175_27135"
     CDS             complement(1370..1930)
                     /locus_tag="E3175_RS26505"
                     /old_locus_tag="E3175_27135"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /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_000067487.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKKQLDTLSTTVSMQFSTTEAELSRQQKKLLWRVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            complement(<1959..2618)
                     /locus_tag="E3175_RS28280"
                     /old_locus_tag="E3175_27140"
                     /pseudo=""
     CDS             complement(<1959..2618)
                     /locus_tag="E3175_RS28280"
                     /old_locus_tag="E3175_27140"
                     /inference="COORDINATES: protein motif:HMM:NF015397.3"
                     /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(2608..2931)
                     /locus_tag="E3175_RS26515"
                     /old_locus_tag="E3175_27145"
     CDS             complement(2608..2931)
                     /locus_tag="E3175_RS26515"
                     /old_locus_tag="E3175_27145"
                     /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_024132211.1"
                     /translation="MLTIRVTDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2995..3186
                     /locus_tag="E3175_RS26520"
                     /old_locus_tag="E3175_27150"
     CDS             2995..3186
                     /locus_tag="E3175_RS26520"
                     /old_locus_tag="E3175_27150"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /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_000165979.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNDLDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(3268..3348)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.805"
                     /coverage="93.0"
                     /evalue="8.68e-18"
     Typing          complement(1048..2618)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.817"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gtcaggagta aaaagccgca cagatgtaaa aacagcgcac ccgataaaca gcacacacgc
       61 ggacactgtc acaggcgcgt aagtgcacaa tgcttgcatc tgtgactctt ccgcttcctc
      121 gcccactcgc tcactacgtt cggtcgctgg ggctgcggcg agcggtggga tcactctcgt
      181 tgtgatgcag atccgttttt ttttttgcac tggagttatc aggagttgcg gtgcacatgg
      241 gatcgtgcga tatgccggat ggtgaaaggt tggagggaac ggcaacaact cacccctccc
      301 agtgaaggga cgggtagttt gccgctctcg atatgccgga cggagccaag gccatcgatc
      361 acggggcgcg tcagtggaag aacccgcgcc tgcgtgacgt atgcgtcttc gccgcaccat
      421 ctcacccgtc acgccaccac ataccgggaa ctgccgccaa ggtctaactc aaccaatcta
      481 gccgcgctac atacggtttt tgtggcaact catcaggtgt ccgctgtcga tgaaactctc
      541 tgcgccggta gcggaactct cacgcgtgcg gtcgccgtcg tcacagctcc cccaaccgca
      601 aacgattctc gcaaatacgc aagtatctgc aaaaacaggt ttttttcggg gttcctggga
      661 gactgtgctg ttgaaaaatt cttgaagaat acagaaggct catgcaaact gaatgaactg
      721 gtttctgttg tggatctcaa cagtttccac aggaacattg aggaggtcag agacctcaat
      781 gaacccgaaa cagctcgcct tcctggcgag ctgttttcgt tctacgcccg ccgacgaaag
      841 atcgcaagtg caataacgag atttttcacg tctttacgct caaaaagtaa aaaaaccatg
      901 ttttcccctg gctgaatccc caaaaacgcg tgaaatgcgt tttcaggatg ttgcatagct
      961 atgcacaaat acggcacacg atttgtttcg ctcgccccag ccgtcgaact ggtcaaaatg
     1021 gcaagatttc gtcacttccc cggtcacatc tccattgatg gcccactccg aacccgtgcc
     1081 gcgcgttcct gtacctcatg tctgtaccgg gcacgctcct gttcatccct tagctgttgt
     1141 tcgcgataaa taaccgactc aagcgatcca cttgcccggc taatctctgc acctgctgac
     1201 tcaatatcac gacgcgctcg ttcagtatcg cgttgttccg ttgcgtaacc tcgtgcatct
     1261 tctgcaattc cgcgaaggcg ctctcccact cgttcagccg ccgcatatag tcctgttgca
     1321 aatgctctaa ggcgttcagc aaatgccctt ccagttccgt catactcgtt tactccctga
     1381 ccagcctcac ggcgttcttg tcgcccaccg tccaggtgtt ttcccctttc accccgtccg
     1441 gcaacaccag aaatttcccg ttctcgccat tgacgaacgt caccccccag gtttttgcct
     1501 cgagtttcgc cagcgtgttt tcctgctctc tgatagtcag gatatttttc gcaatcttgc
     1561 tttcctgcca ctccatcagc ccccagcacc ccaggaaaat gccgcccgtg acgctgagcg
     1621 cggtcagcgc cggaaacagt atccgccctt tgatcacccg ccagagcagt tttttctgct
     1681 gccgggacag ttcggcctct gtggtgctga actgcatgct cacggtggtg ctcagcgtat
     1741 ccagttgctt tttcacggat gttgtatgtt cgctgatagc gtctctgatt ttctgcctgt
     1801 ttaagctcaa tgccttgtct acagactctt cgagcttcct gaactcgctg ttcagcatgt
     1861 tctcggtaga agcggctcgc tctttcagtt tcttctcgaa gtctgttccc atttgtaaaa
     1921 gattgctcat acagcgcccc ctttagcctg agattccgcc ccccctccgg gtcggcaata
     1981 ctgatgctgc ttttggttgt cctcaccacc tcaaaacctg ccgctgtaag cgcctctgtg
     2041 acatcctgac gcgtttttat tgctccggca tggtaaagag cctcaagacc ccgtgtaatc
     2101 gcttctgcgg cctcctgttt cgcttttggc agattatttg gcgtgacaag cgtccgtctg
     2161 ttctccggtg cgttcgggtc acgcagcccg taatgatgat taaccagcgt ctgccaggca
     2221 tttatcctcg gcctgtccgc gcggtcgtag tacggctgga ggcgcttacc gctctgtagc
     2281 tccatgttcg ggatgacaaa attcagttcg agccgcccct tatcctggtg ttccacccag
     2341 agaatgctgt actggtcttt ttcgagaccg ggcataagaa cacgctcaaa gctcgtcatc
     2401 actctttcgc gttcacccgg cggtaactcc ttctccgcga acgacagaac gcctgaagtg
     2461 tatttcttcg aaaatggcgt ggaatcaatg agttctcgca cttcttccgg gttaccccgg
     2521 agcaccgttg cgccttcgcg gttacgctcc cgccccagca ggtaatcgac cgggccactt
     2581 ccaccgcctt tccccctggc atgaaattta actatcatcc cgtaccccct gttccctgac
     2641 agcctgccgc aactggcgca attcaccctc gatggccatc agtgcggcca ccacatgaac
     2701 ccggtcaatc gaagaccact gaccgctgtt caccttccgg gctgtctggt tcaggttgtt
     2761 cccgatggca gccagatgcc gcagcaatgg cggcgatagt gtcggcagtt ttcctgtgcg
     2821 tgcaaccggc tcccccagac agacccgccg catccattcc gccagtcgtt taccctcgca
     2881 gcgttccagt aaccgggcgt gctcctcatc ggtaacccgt atcgtgagca tcttctcgcg
     2941 tttcatcggt atcattcccc ctaacaaatc ccccatacaa ggagccttaa gaccatgacc
     3001 aaacaggaaa aaacagccct taacatggct cgctttatca gaagccagac gctaaccctg
     3061 ctggaaaaac tcaacgatct ggacgcggac gaacaggcag acatctgcga atcacttcac
     3121 gaccacgccg acgaactcta ccgcagttgc ctcgcacgct tcggcgatga cggtgaaagc
     3181 aactgaaaca tgcagctccc ggagacgttc acagcttgcc tgtgagcgga tgccgggagc
     3241 agacaagccc gccagggcgc gtcagtgcgg gtgtcggggc gcagccctga cccagttcac
     3301 agagcgatag cgatgtgtat actggcttat ctcattttgc atcggtgcag agtggatggg
     3361 aagtgcacca t
//
