LOCUS       NZ_CP039839             4656 bp    DNA     linear   CON 14-NOV-2023
DEFINITION  Escherichia coli O55:H7 strain USDA5905 plasmid pUSDA5905_5.
ACCESSION   NZ_CP039839
VERSION     NZ_CP039839.1
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 4656)
  AUTHORS   Bono,J.L.
  TITLE     Comparison of 54 complete closed STEC O157:H7 genomes
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4656)
  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
            CP039839.1.
            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..4656
                     /organism="Escherichia coli O55:H7"
                     /mol_type="genomic DNA"
                     /strain="USDA5905"
                     /serotype="O55:H7"
                     /isolation_source="Food (meat)"
                     /db_xref="taxon:244320"
                     /plasmid="pUSDA5905_5"
                     /collection_date="1994"
     gene            <1..98
                     /locus_tag="E3175_RS26525"
                     /old_locus_tag="E3175_27155"
                     /pseudo=""
     CDS             <1..98
                     /locus_tag="E3175_RS26525"
                     /old_locus_tag="E3175_27155"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_032489893.1"
                     /note="incomplete; too short partial abutting assembly gap;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=3
                     /transl_table=11
                     /product="class A beta-lactamase"
                     /name="class A beta-lactamase"
     gene            complement(246..449)
                     /locus_tag="E3175_RS26530"
                     /old_locus_tag="E3175_27160"
     CDS             complement(246..449)
                     /locus_tag="E3175_RS26530"
                     /old_locus_tag="E3175_27160"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000427298.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="retron Se72 family effector protein"
                     /protein_id="WP_000427298.1"
                     /translation="MENGFVNFYDHVKGYGFIRRERGRDVFFRYDDFLFLGHDVDICKG
                     ILVRFKLEKTDKGFKAVAIQKV"
                     /name="retron Se72 family effector protein"
     gene            complement(454..1593)
                     /locus_tag="E3175_RS26535"
                     /old_locus_tag="E3175_27165"
     CDS             complement(454..1593)
                     /locus_tag="E3175_RS26535"
                     /old_locus_tag="E3175_27165"
                     /EC_number="2.7.7.49"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761319.1"
                     /GO_function="GO:0003964 - RNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="reverse transcriptase family protein"
                     /protein_id="WP_024174670.1"
                     /translation="MNKPRFNGTPVASLDSLSAMLGIERKRLDWIVKSVSMSYKQFKVE
                     TGKNKKERQIFEPKRSLKGIQKKINKEIFEKIDYPHYLHGALSGRDYISNAAVHTRKRT
                     VICLDITNFYPSISKKDVCSIFKNLMRFSPDVSLCLTELVTLNNKVPQGGCCSSYIANL
                     LFFNSEYNIYNRLKSMGLSYSRLLDDITISSDKDLSSEEKTKVIKLVHGMVNQYRLSIN
                     ESKTTIEHSKDSSSKLSVTGLWVKHGVPKLTKENRRYIRYLVYICKKQGAYERHTKEYH
                     DLWNRCSGKVAQMSRLGHVQAVELRAILSEIMPVYDDYKISKLKLMAKHYLNKFTPPLT
                     DDQIRKIDRMLYDFDIVGRTNKNLAKLYRRKLVALLPDR"
                     /name="reverse transcriptase family protein"
     gene            complement(2167..2373)
                     /locus_tag="E3175_RS26540"
                     /old_locus_tag="E3175_27175"
     CDS             complement(2167..2373)
                     /locus_tag="E3175_RS26540"
                     /old_locus_tag="E3175_27175"
                     /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_032321799.1"
                     /translation="MATFDGKVLRDASLKKVATFDGKVLRDASLKKVATFDGQNLRDAS
                     SKIILSADAEVGIVVMAFVAELI"
                     /name="hypothetical protein"
     gene            complement(2756..3079)
                     /gene="mobA"
                     /locus_tag="E3175_RS26545"
                     /old_locus_tag="E3175_27180"
     CDS             complement(2756..3079)
                     /gene="mobA"
                     /locus_tag="E3175_RS26545"
                     /old_locus_tag="E3175_27180"
                     /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            3363..3557
                     /locus_tag="E3175_RS26550"
                     /old_locus_tag="E3175_27185"
     CDS             3363..3557
                     /locus_tag="E3175_RS26550"
                     /old_locus_tag="E3175_27185"
                     /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_001041640.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEAENRTGI"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(4433..>4656)
                     /locus_tag="E3175_RS26555"
                     /old_locus_tag="E3175_27200"
     CDS             complement(4433..>4656)
                     /locus_tag="E3175_RS26555"
                     /old_locus_tag="E3175_27200"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_032495017.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=3
                     /transl_table=11
                     /product="Tn3 family transposase"
                     /protein_id="WP_174846761.1"
                     /translation="NAVVLWNTIYMQAALDHLRAQGETLNDEDIARLSPLCHGHINMLG
                     HYSFTLAELVTKGHLRPLKEASEAENVA"
                     /name="Tn3 family transposase"
     Typing          complement(3089..3328)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.755"
                     /coverage="100.0"
                     /evalue="7.66e-118"
     Typing          3593..4114
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.476"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          complement(2760..3079)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="3.1e-62"
ORIGIN
        1 gtatcgtagt tatctacacg acggggagtc aggcaactat ggatgaacga aatagacaga
       61 tcgctgagat aggtgcctca ctgattaagc attggtaact gtcagaccaa gtttactcat
      121 atatacttta gattgattta aaacttcatt tttaatttaa aaggatctag gtgaagatcc
      181 tttttgataa tctcatgacc aaaatccctt aacgtgagtt ttcgttccac tgagcgtcag
      241 accccttata ccttttgaat cgctacagct ttaaaccctt tatctgtttt ttctaattta
      301 aacctaacta aaataccttt acatatatcg acatcatgcc ctaaaaacaa aaaatcatca
      361 taccgaaaga aaacatcacg tccacgctca cgccttataa agccataccc tttaacatgg
      421 tcataaaaat taacaaatcc attttccata taatcaccta tctggaagta atgccacgag
      481 cttacgtcta tatagttttg caagattctt attagtccgc cctactatat caaaatcata
      541 gagcatccta tctattttcc taatctgatc atcagttaaa ggaggcgtaa acttatttag
      601 atagtgctta gccatcaact ttaatttaga tatcttgtaa tcatcataaa ctggcattat
      661 ctcagaaaga atcgccctca attcaaccgc ctggacatgc ccaagcctcg acatttgagc
      721 aaccttgcca gagcatctat tccataaatc atggtactct ttcgtatgac gttcataagc
      781 accttgtttt ttacatatat aaactaaata cctgatataa cgtctatttt cttttgttaa
      841 cttaggaaca ccatgcttta cccacaaccc agtgacacta agtttagaag acgaatcttt
      901 tgagtgctct atcgttgtct tactttcatt tattgaaagt ctgtactgat tcaccattcc
      961 gtgaacgagt tttattactt ttgttttttc ctctgatgaa agatccttat cagaagatat
     1021 agtaatatca tctaaaagcc ttgaatatga aagtcccata gacttcaatc tattatagat
     1081 attatactca ctattaaaaa ataaaagatt tgcaatataa ctagaacagc acccaccctg
     1141 agggacctta ttattcaacg tcacaagttc cgttaagcat aaagaaacat caggagaaaa
     1201 acgcattaaa tttttaaaaa tagaacaaac atctttttta ctaatgctgg gataaaaatt
     1261 ggtgatatca agacatataa ctgttctttt cctagtatga acagcggcat tagatatata
     1321 atcgcgacca cttaacgccc catgcaaata atgagggtaa tcaattttct caaaaatctc
     1381 tttatttatt tttttttgaa ttcctttcaa agatctcttg ggttcaaaaa tttgcctttc
     1441 ttttttattc ttccctgttt caaccttaaa ctgcttgtac gacatcgata cagacttgac
     1501 tatccagtcc aatctttttc tttctatgcc taacatcgca gataaagaat ccaaagatgc
     1561 aacaggagtt ccattaaacc tgggtttatt catgatgttt gagttaaaag tcgattagtt
     1621 aaaaagtttc gatacgtaat ctattacttt aaacataatc aagcacatag aaaacaaaaa
     1681 ctgtgttttt ttcagtgcct ccagagagcc aacctctctt tttttcttca tctgaccgtc
     1741 tccagaacaa gatgaagagc tcttggttac gttaatgttg atgttgataa taaacatgat
     1801 gcaactccta ttggttatga aattttgcca gaccagtagg aaagcaagga aaaactctat
     1861 tggctctttg ggacttttaa ctcacattgc cagacaatcg tcgctattct tttagtgctg
     1921 atacacgctc aggggcgttc tcaccattaa ttagcggcca ggccggtcat gatctcatgc
     1981 gagatcgcct taaaaacaag gcatcggttt ccttgcgcaa catacacgta accatttgtt
     2041 aaagagcgag agccaggcgt ggttcgcccg cttcgctgat tattataaag ttttttatct
     2101 ttctgtcacc aacaagaaag cgccttatcc tgccagcgat aggctaaaag gtatgcagca
     2161 tgagattcaa atcaactcag ctacaaaggc cataacaaca atcccaacct cagcatcggc
     2221 actcaggata atttttgaac tagcatctct taaattctga ccgtcaaagg ttgctacttt
     2281 ttttaaagag gcatccctta aaaccttgcc atcaaaagtc gccacttttt ttaaagaggc
     2341 atcccttaaa accttgccat caaaagtcgc cacttttttt aaagaggcat cccttaaaac
     2401 cttgccatca aaagacgcta tttttctcga aaaggcatct cttaaggttt taccgtcaaa
     2461 ccgagcaacg gtttttaagt cattgttttt ttattgaaat attcatttct caccaatagt
     2521 aatttaacca attgtattta ccataatccc ttaattgtac gcaccacaga atcgcgctga
     2581 gcgcgattct gacacagaca ctgcaaaaag agatgtttta ccctaagaaa accggggaaa
     2641 tgcgtcagga tcgttttcag ctcgctgcat agctatgcat gaaagcgagt ggtgatcact
     2701 ttgggagctt acagtgttca taccgtctgt tttcgacagt tttctcccct ggaagctaat
     2761 ctgccataag cctggataac agggcacggt gatactccgt aatagcgatc agcacctccg
     2821 catactccct gtccccgaca cgcttgccgt cgataaagag ttttttctgt aacgccccca
     2881 gtctcataac ttctttcagt acccgatcat cagtcagtga gttaactttc ttaccgagag
     2941 ctgccgcccg taaaaaaccg gaaacggtct tgccgcattc agcagccctt tttctgattt
     3001 cctggtcttc ttctgccgtc agacgaacag ggcgactgat agcccgcctg cgcgtattac
     3061 ttccacttcg ttttgtcata aaacatggct ccgtatctga catgggtgtc ggggcaaagc
     3121 cctgaccagg gtaattgtaa tagcgtgcat gtatgcgcgg tataacaatt gcacatcctg
     3181 tcctgtcagc aagctcgaat taccgacaaa ggcacggcag ttttttggca gtgacagtgt
     3241 tgtctgacag aaatgcccgt caaagagtca gacagcagaa taccgacggt aaaacagtcg
     3301 aaaagtggta cacgatataa tcacacaacg cagatgacag aaagaacgga gaaaacagaa
     3361 agatgaacaa gcagcagcaa accgtactca acatggcagg attcataaaa agccagagcc
     3421 tgacgctgct cgaaaaactg gacgcacttg atgctgacga acaggccgcc atgtgtgaga
     3481 agctgcacga actcgcggaa gaacttcaga acagcataca gacacgcttt gaagcggaaa
     3541 atcgcaccgg gatataacgc atccggacag gatgcagaac ggcatagagg agcgtaagga
     3601 gaaaatgtca cataaggcgc tcttccgctt cctcgctcac tgactcgcta cgctcggtcg
     3661 ttcgactgcg gcgagcggtg tcagctcact caaaggcggt aatacggtta tccacagaat
     3721 caggggataa cgccggaaag aacatgtgag caaaaagccg aagccaggga caaaggccgc
     3781 gccgatggcg tttttccata ggctccgccc ccctgacgag catcacaaaa accgacgctc
     3841 aagtcagagg tggcgaaacc cgacaggact ataaagatac caggcgtttc cccctggaag
     3901 ctccctcgtg cgctctcctg ttccgaccct gccgcttacc ggatacctgt ccgcctttct
     3961 cccttcggga aacgtggcgc tttctcatag ctcacgctgt tggtatctcg gcccggtgta
     4021 ggtcgttcgc tccaagctgg actgtatgca cgaacccccc gttcagtccg accgctgcgc
     4081 cttatccggt aactatcgac ttgaatccaa accgagaaga cacgacttat cgccactggc
     4141 agcagccact ggtaaccgaa ttagaggagt tagccttgaa gtcatgcgcc tgttaaggct
     4201 aaactgaaag aacaagtttt ggtgactgcg ctcctccaag ccagttacct cggctcaaag
     4261 agttggtagc tctgagaacc ttcgaaaaac cgccctgcaa ggcggttttt tcgtttacac
     4321 agcaagagat tacgacgaga tagaaaggat ctcaagttct catatcataa aaacaagctg
     4381 acacatccac gatgttatag gggtctgacg ctcagtggaa cgaaaactca cgttaagcaa
     4441 cgttttctgc ctctgacgcc tcttttaatg gtctcagatg acctttggtc accagttctg
     4501 ccagcgtgaa ggaataatgg ccgagcatat tgatatgtcc gtggcaaagc ggggagaggc
     4561 gtgcgatatc ttcatcattc agtgtttcac cctgcgcccg gagatgatcc agagctgcct
     4621 gcatataaat agtgttccat aacacgacgg cgttag
//
