LOCUS       NZ_CP104502             4145 bp    DNA     circular CON 07-OCT-2023
DEFINITION  Escherichia coli strain E9 plasmid p2, complete sequence.
ACCESSION   NZ_CP104502
VERSION     NZ_CP104502.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN30789312
            Assembly: GCF_025369815.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4145)
  AUTHORS   Feng,A., Leigh,S.A., Akter,S., Wang,H., Pharr,T.G., Evans,J.,
            Branton,S.L., Landinez,M.P., Pace,L. and Wan,X.-F.
  TITLE     Genomic Diversity, Pathogenicity and Antimicrobial Resistance of
            Escherichia coli Isolated from Poultry in the Southern United States
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4145)
  AUTHORS   Leigh,S.A.
  TITLE     Direct Submission
  JOURNAL   Submitted (10-SEP-2022) Bond Life Science Center, University of
            Missouri, University of Missouri, Columbia, MO 65201-8522, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.9b
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100%x
            Sequencing Technology             :: Oxford Nanopore; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 10/07/2023 07:23:14
            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)                     :: 5,355
            CDSs (total)                      :: 5,232
            Genes (coding)                    :: 5,026
            CDSs (with protein)               :: 5,026
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 206
            CDSs (without protein)            :: 206
            Pseudo Genes (ambiguous residues) :: 0 of 206
            Pseudo Genes (frameshifted)       :: 76 of 206
            Pseudo Genes (incomplete)         :: 141 of 206
            Pseudo Genes (internal stop)      :: 35 of 206
            Pseudo Genes (multiple problems)  :: 43 of 206
            Pseudo Genes (short protein)      :: 3 of 206
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP104502.1.
            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..4145
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="E9"
                     /isolation_source="Broiler"
                     /host="Poultry"
                     /db_xref="taxon:562"
                     /plasmid="p2"
                     /geo_loc_name="USA"
                     /collection_date="2017-06-13"
                     /collected_by="USDA"
     gene            join(3931..4145,1..928)
                     /gene="wzz(fepE)"
                     /locus_tag="N5O75_RS26620"
                     /old_locus_tag="N5O75_26625"
     CDS             join(3931..4145,1..928)
                     /gene="wzz(fepE)"
                     /locus_tag="N5O75_RS26620"
                     /old_locus_tag="N5O75_26625"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010435173.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_process="GO:0009103 - lipopolysaccharide biosynthetic
                     process [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="LPS O-antigen length regulator Wzz(fepE)"
                     /protein_id="WP_021544858.1"
                     /translation="MSAMDFKKNTDLDFPRYATPAVSTKEIDLLGLLDVLLAAKKRIVT
                     IVLAFAVVGLAIAFLIPQKWTSKAVITPAEQTQWNTLRQMMVTLQVLDVDAKVSRGDVF
                     NLFIKKFQSQSLLEEYMKTSPYVMSQLEGTEVDPLELHRAVVNIAEKMKATDNTQVKDA
                     DKAPYTSWTLSFTAPTAGDAQTVLEGYINYISRIVEQETMENIRNQITLKTKVVQQQLE
                     LDRVRLTNIHNTNLQRLNYSLEVANAAGIKKPVYSNGQAVKDDPDYSVALGADGIAQKL
                     QIEKNLKDVAELNADFQNREYYLTQLQKLSVEDVKLEPFRYQLSPSLPVKKDGPGKALI
                     VLLAGILGGLFACGSVLLREAMLSRNPLPEPITAVTPATE"
                     /name="wzz(fepE)"
     gene            complement(966..>1208)
                     /locus_tag="N5O75_RS26625"
                     /old_locus_tag="N5O75_26630"
                     /pseudo=""
     CDS             complement(966..>1208)
                     /locus_tag="N5O75_RS26625"
                     /old_locus_tag="N5O75_26630"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003862821.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="cupin domain-containing protein"
                     /name="cupin domain-containing protein"
     gene            <1205..1387
                     /locus_tag="N5O75_RS26630"
                     /old_locus_tag="N5O75_26635"
                     /pseudo=""
     CDS             <1205..1387
                     /locus_tag="N5O75_RS26630"
                     /old_locus_tag="N5O75_26635"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007798797.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="NINE protein"
                     /name="NINE protein"
     gene            2573..2686
                     /locus_tag="N5O75_RS26635"
                     /old_locus_tag="N5O75_26640"
     CDS             2573..2686
                     /locus_tag="N5O75_RS26635"
                     /old_locus_tag="N5O75_26640"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_071778980.1"
                     /translation="MHEPPVQSDRCVFSGNYRLESKPERHDKAPLAAATGN"
                     /name="replication initiation protein"
     gene            2994..>3125
                     /locus_tag="N5O75_RS26640"
                     /old_locus_tag="N5O75_26645"
                     /pseudo=""
     CDS             2994..>3125
                     /locus_tag="N5O75_RS26640"
                     /old_locus_tag="N5O75_26645"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013578013.1"
                     /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="zinc-ribbon domain-containing protein"
                     /name="zinc-ribbon domain-containing protein"
     gene            complement(3274..3390)
                     /locus_tag="N5O75_RS26645"
                     /old_locus_tag="N5O75_26650"
     CDS             complement(3274..3390)
                     /locus_tag="N5O75_RS26645"
                     /old_locus_tag="N5O75_26650"
                     /inference="COORDINATES: protein motif:HMM:NF013752.3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001407452.1"
                     /translation="MKARYKGLLKNDNQLAMLFTLANLFRADQMIRQWERSH"
                     /name="hypothetical protein"
     gene            complement(3353..3736)
                     /locus_tag="N5O75_RS26650"
                     /old_locus_tag="N5O75_26655"
     CDS             complement(3353..3736)
                     /locus_tag="N5O75_RS26650"
                     /old_locus_tag="N5O75_26655"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003117291.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS5/IS1182 family transposase"
                     /protein_id="WP_021544857.1"
                     /translation="MSHQLTFADSEFSSKRRQTRKEIFLSRMEQILPWQNMVEVIEPFY
                     PKAGNGRRPYPLETMLRIHCMQHWYNLSDGAIEDALYEIASMRLFARLHESQHPGQGGA
                     PISHHQATVRLRESQIQGVAEKR"
                     /name="IS5/IS1182 family transposase"
     Typing          2302..2690
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.153"
                     /coverage="91.0"
                     /evalue="1.04e-173"
ORIGIN
        1 gccggccgag cagacgcagt ggaacacgct gcgccagatg atggtgacgc tgcaggtgct
       61 ggacgtcgac gcgaaggtga gccgtggaga cgtgtttaac ctgttcatca aaaagtttca
      121 gtcgcagtcg ctgctcgaag agtacatgaa aacctccccg tacgtgatgt ctcagctgga
      181 aggcaccgag gtagacccgc tggagctgca tcgcgcggtg gtgaatattg ctgagaaaat
      241 gaaagcgaca gataacacgc aggttaaaga cgcagacaaa gcgccgtata cctcatggac
      301 gctgagcttt accgccccga cggcgggaga cgcgcagacg gttctggaag gttacatcaa
      361 ctatatctcc cgcattgttg agcaggagac gatggaaaat atccgtaacc agatcacgct
      421 gaaaacgaaa gtcgttcagc agcagctgga gctggatcgc gtgcgtctga ccaatatcca
      481 caacaccaac ctgcagcgcc tcaactattc gctggaagtg gcgaacgcgg caggcattaa
      541 gaagccggtt tacagcaacg gacaggcggt aaaagacgat cctgactact ccgtggcgct
      601 gggtgctgac ggtattgcgc aaaagctgca gattgaaaag aatctgaagg acgtggccga
      661 gctgaatgcg gatttccaga accgtgaata ctatctgact cagttgcaaa aactgtccgt
      721 ggaagacgtg aagcttgaac ccttcaggta tcagctttca ccgtcactgc cggtgaaaaa
      781 agacggtccg ggcaaagccc tgattgtgct gctggcaggg attctgggcg gcctgtttgc
      841 ctgcggcagc gtgctgctgc gtgaggcaat gctctcgcgt aatccgttgc cagagccgat
      901 aacggccgta acgccagcaa cagagtaacg acgatattaa aaaggcgctg attcagcgcc
      961 tttttttatt tcaggaaatc gtcgcgcacc ggcgtaaagg tatccagaag ggtgccgggc
     1021 ttcaggcaaa tgcagccgtg catcacgtgc ggcgctttat agagcgtatc gcccgccgtc
     1081 acgatctgct tttcttcacc tatcgtaaac tcgaactccc cggagagcac ataggtaagc
     1141 tgttcatgcg ggtgattgtg catcgggcca atcgcaccct gctcaaaatt gacctccacc
     1201 gccatcatct ttcttagcat tcttccttgg tggatttggc gtacataaat tttacttagg
     1261 taaaatagga cagggattcc tgtatctaat tttttgctgg acattcatac ccgcgatcat
     1321 cgcgtttatt gagtttatta tttatctatg cgattccgat gaaaaattcg caagaaaata
     1381 tggctaactc atagcaaaaa agccctgcgg ggcttttttt gtaccagtct gtgaggcaga
     1441 tttaccataa catccgttgc gtgcaccgcc tgagaggctc tcagggcgtt tctgggtctt
     1501 cctgcctgtt tccgacactt ccctgtgcct atatcgtgaa aaaacgcgcc tgatgattct
     1561 ggcgcgtctg catggctatg cacacacatg catggccggg attttagcgg ctaaaatccg
     1621 gctggacgcc caaaagcacc actgaacctc acgaataacg cctcacgggt gtgcagttta
     1681 ctgtgcggcc gtgaggcgtt ggccaggccg tcaggcatgg ctggatttat tgctaagggg
     1741 gtcggattta acgtggatga atcagcacgc agtgatgaac gggattcgga aggggcaccc
     1801 ttgcggcgcg gcgatgtata catcgctaac gtgccttggt catttattgc aagaagggag
     1861 aggtagcatt ttgatagcaa aaaagtagca aaaggatagc aaccgaaaga ccagaagact
     1921 ctggagatag caaaaaagta gcaaaatggt agcaaaaaga tagcaaacat gcgggagcta
     1981 accaggagtc tttagcgggc cggcggtact ccaaaaacac atcttgtccc gctgttttgt
     2041 gaataagcca gcatagctgt gggcacaaaa catttcctgt ccgctgcttt aacctttgta
     2101 atccaggaac gtcaggtgac gtcactttgc ggcgttagcc ctatcctgca tcgtattaaa
     2161 aaatgcagca ctggcgcgta cggtgccgaa gataagtccg gggatattcc gcttcctcgc
     2221 tcactgactc gctacgctcg gtcgttcggc tgcggcgagc ggagggaacg gagacattaa
     2281 ggcacaggca atgagagagg atcgagaggc aaaagaaaag gccgcggcgt tgccggtttt
     2341 ccataggctc cgcccccctg acaagcatca cagaatctga cgctcaaatc agtggtggcg
     2401 aaacccgaca ggacttaaag ataccaggcg tttccccctg gtggctccct cgtgcgctct
     2461 cctgttcctg cctttcggtt taccggtgtc attccgctgt tatggccgcg tttatctcat
     2521 tccacgcctg acactcagtt ccgggtaggc agttcgctcc aagctggact gtatgcacga
     2581 accccccgtt cagtccgacc gctgcgtctt ctccggtaac tatcgacttg agtccaagcc
     2641 ggaaagacac gacaaagcgc cactggcagc agccactggt aactgattta gaggagttag
     2701 tcttgaagtt atgcgcctgt taaggctaaa ctgaaagaac agatttggtt actgcgctcc
     2761 tcataagcca gttaccacgg ttcaaagagt tgcagctctg agaaccttcg aaaaaccgcc
     2821 ttgctgggcg gttttttcgt ttactgagca agagattacg acgctacaga aaggatctca
     2881 agaagatcct tcaccataat ggaaatctat cccacccgag catataggat gcatatcgtt
     2941 ataaaacatc ggatattatg catcccaact aaaaataagc tcgaggataa aaaatgagtt
     3001 caatggttta ctgccgagga tgcggcaagg aaatacacga aacagcaaag tcatgcccac
     3061 actgcggagc cacaaacgcc tcttcaggtt caggtgaaaa aagtagaatc gcagccgcgc
     3121 tattagggaa ggtgcgaata agcggggaaa ttcttctcgg ttgactcagt catttcattt
     3181 cttcatgttt gaaccgattt ttttctcccg taaatgcctt gaatcagcct atttagaccg
     3241 tttcttcgcc atttaaggcg ttattcccag tttttagtga gatctctccc actgacgtat
     3301 catttggtcc gcccgaaaca ggttggccag cgtgaataac atcgccagtt ggttatcgtt
     3361 tttcagcaac cccttgtatc tggctttcac gaagccgaac tgtcgcttga tgatgcgaaa
     3421 tgggtgctcc accttggccc ggatgctggc tttcatgtaa ccgggcaaac agacgcatgg
     3481 aggcgatttc gtacagagca tcttcgatcg cgccatcgct caggttgtac caatgctgca
     3541 tgcagtgaat gcgtagcatg gtttccagcg gataaggtcg ccggccatta ccagccttgg
     3601 ggtaaaacgg ctcgatgact tccaccatgt tttgccatgg cagaatctgc tccatgcggg
     3661 acaagaaaat ctcttttctg gtctgacggc gcttactgct gaattcactg tcggcgaagg
     3721 taagttgatg actcatgatg aaccctgttc catggctcca gatgacaaac atgatctcat
     3781 atcagggact tgttcgcacc ttccctaaat ctgatagtcg gtctacagat agatcaatct
     3841 ggcgttcaga ttattcttac tttcttgtat catccgacca ctgcaaccaa tcaggcagaa
     3901 atttactgcg ctccaaaaag aagaacggtt atgtcagcga tggatttcaa gaaaaacacg
     3961 gacctcgatt ttccccgtta tgccactccg gcggtaagca ccaaagagat agatctcctg
     4021 gggttgttag acgtacttct ggcagccaaa aaacgtattg tgacgatcgt cctggcgttc
     4081 gccgtagtag ggttggccat tgcgttttta atcccgcaaa aatggaccag taaagccgtg
     4141 atcac
//
