LOCUS       NZ_CP104531             4496 bp    DNA     circular CON 06-OCT-2023
DEFINITION  Escherichia coli strain E8 plasmid p5, complete sequence.
ACCESSION   NZ_CP104531
VERSION     NZ_CP104531.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN30789311
            Assembly: GCF_025369695.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4496)
  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  JOURNAL   Unpublished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 4496)
  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                   :: 10/06/2023 04:00:05
            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)                     :: 4,961
            CDSs (total)                      :: 4,843
            Genes (coding)                    :: 4,556
            CDSs (with protein)               :: 4,556
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 287
            CDSs (without protein)            :: 287
            Pseudo Genes (ambiguous residues) :: 0 of 287
            Pseudo Genes (frameshifted)       :: 107 of 287
            Pseudo Genes (incomplete)         :: 175 of 287
            Pseudo Genes (internal stop)      :: 49 of 287
            Pseudo Genes (multiple problems)  :: 43 of 287
            Pseudo Genes (short protein)      :: 3 of 287
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP104531.1.
            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..4496
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="E8"
                     /isolation_source="Pullet"
                     /host="Poultry"
                     /db_xref="taxon:562"
                     /plasmid="p5"
                     /geo_loc_name="USA"
                     /collection_date="2017-06-05"
                     /collected_by="USDA"
     gene            complement(360..551)
                     /locus_tag="N5O73_RS24635"
                     /old_locus_tag="N5O73_24640"
     CDS             complement(360..551)
                     /locus_tag="N5O73_RS24635"
                     /old_locus_tag="N5O73_24640"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041614.1"
                     /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_047402702.1"
                     /translation="MNKQQKTAVNMAKFIQDQSLLLLDRLNELDLDHEADFCEKLHEDA
                     ERLYRSLSARLNDQQDGA"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1029..1247
                     /locus_tag="N5O73_RS24640"
                     /old_locus_tag="N5O73_24645"
     CDS             1029..1247
                     /locus_tag="N5O73_RS24640"
                     /old_locus_tag="N5O73_24645"
                     /inference="COORDINATES: protein motif:HMM:NF024252.3"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix transcriptional regulator"
                     /protein_id="WP_261246588.1"
                     /translation="MDKNLKLLGESIKKARTLLGISQEELAFRSMLHRTYISSVERGER
                     NISFLNLIKIAKALEISPSELIEGIIC"
                     /name="helix-turn-helix transcriptional regulator"
     gene            1241..1840
                     /locus_tag="N5O73_RS24645"
                     /old_locus_tag="N5O73_24650"
     CDS             1241..1840
                     /locus_tag="N5O73_RS24645"
                     /old_locus_tag="N5O73_24650"
                     /EC_number="3.1.21.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002759004.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ScaI family restriction endonuclease"
                     /protein_id="WP_075043415.1"
                     /translation="MLNNPHPYLNKSKEEWLNITNELIKSHPLTEKEIVDTCLSAWDDM
                     FNTEIGGARLKIGRDIFPTPQIIGYLLHELIPAEIEKKHPSMWRKDESAHEKDLVCLEN
                     DYFSTEVKTSSNKNQIFGNRSYAQESISDKKSKNGFYITINFTTPKKDVEEPKVNIIRF
                     GWLDHTDWIAQKAASGQQARLSPDAYLYKLKVLYKS"
                     /name="ScaI family restriction endonuclease"
     gene            complement(1826..2674)
                     /locus_tag="N5O73_RS24650"
                     /old_locus_tag="N5O73_24655"
     CDS             complement(1826..2674)
                     /locus_tag="N5O73_RS24650"
                     /old_locus_tag="N5O73_24655"
                     /EC_number="2.1.1.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015080220.1"
                     /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_065806342.1"
                     /translation="MFDRIKALLGSPAYEHTDVLIYNMDCLEAMRKLPADMVDIAVTSP
                     PYNIGKSYENIIALKDYISWCSNWMSELHRISKDDGSFWLNVGYLEVENKGLAVPIPYL
                     LWDKSDFYLIQEIVWNYSAGVACKKRLSPRNEKILWYVKNQDNYKFNLDDIRDPNVKYP
                     NQKKNGKLKCNPLGKNPSDVWQISKVTSGKNRSSKERTEHPAQFPLEMIDRIIKAGSNN
                     RDLVIDPFMGSGTTAIAALKNGRKVIGFEVNSDYVKIIANRIDEFYKLKSEIGIEPLAL
                     I"
                     /name="site-specific DNA-methyltransferase"
     gene            complement(2667..2834)
                     /locus_tag="N5O73_RS24655"
                     /old_locus_tag="N5O73_24660"
     CDS             complement(2667..2834)
                     /locus_tag="N5O73_RS24655"
                     /old_locus_tag="N5O73_24660"
                     /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_157829372.1"
                     /translation="MKKRGQVGGKISRGGGRPKGSVSFGSINSQKPWEDIGISRSTYYR
                     YLSIKKVSDV"
                     /name="hypothetical protein"
     gene            3216..3329
                     /locus_tag="N5O73_RS24660"
                     /old_locus_tag="N5O73_24665"
     CDS             3216..3329
                     /locus_tag="N5O73_RS24660"
                     /old_locus_tag="N5O73_24665"
                     /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="hypothetical protein"
                     /protein_id="WP_059446996.1"
                     /translation="MHEPPVQSDRCALSGNYHLESNPERHDKAPLAAATGN"
                     /name="hypothetical protein"
     gene            complement(3595..4037)
                     /locus_tag="N5O73_RS24665"
                     /old_locus_tag="N5O73_24670"
                     /pseudo=""
     CDS             complement(3595..4037)
                     /locus_tag="N5O73_RS24665"
                     /old_locus_tag="N5O73_24670"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007966334.1"
                     /GO_function="GO:0046872 - metal ion binding [Evidence
                     IEA]"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="GFA family protein"
                     /name="GFA family protein"
     Typing          427..650
                     /name="rep_cluster_2327"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.556"
                     /coverage="85.0"
                     /evalue="7.880000000000004e-97"
     Typing          2977..3333
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.251"
                     /coverage="83.0"
                     /evalue="2.95e-159"
ORIGIN
        1 atgtaaaatt gttgtaaaag tgttgtaaaa gtgatgtatg aactgaagga gcgatgtaat
       61 tctgtagtca ggaagaataa cccgttcatg caggcatgaa cgatacagtg aggaacgctt
      121 tttttgtcac gatctcccct taacctgcgt aaatcacccg ccatggttga ttatttttca
      181 acctcaaaat ggtcatacac ctaacgcagc tgcgattttt atcgcaactt catgaaaaat
      241 aaataaaaaa gaaaaaataa agggattctg ggtattacta gggtaataat gttaagcacc
      301 aagacaatga aaattaaggc gatgccggta ttactccggt aatacccaga acggagccat
      361 tacgcaccgt cctgctgatc attcaggcgc gctgacaggc ttcggtaaag gcgttccgca
      421 tcctcatgga gtttctcgca gaaatcagcc tcatgatcca gatccagctc attaagcctg
      481 tccagaagaa gcagggactg atcctggatg aatttagcca tgttaacggc tgtcttttgt
      541 tgtttgttca tgaaggcccc ggcgcgaaag tgcttactgt acgttctgat ggttttccgc
      601 ttcctcgctc attcgctcac tccgttcggt catgagtctg cggcgagcgg agggaggata
      661 agcagataac gtaacggtaa gcataacgaa agctaaggac aagggcgaaa aggccacgcc
      721 ccgccggggc gtttttccat aggctccgcc gagaaaaaat tcgcaccact gtgagaattt
      781 ttcgcagtgg atgccggggg tttcgggggg cggcgagccc cctgaaccag tcacggcggc
      841 acctcgtcag aggggacgct gtgtatactg gcttaaagag tagtgcagta tgtcagattc
      901 tgtgctggct gcaaaaaaaa cagccctctt aagaaagggc tgttatctga tataggcttg
      961 tttttgtctc acaccaatga aactcatagt ctgtagaccc aaagtctaca gactgtagat
     1021 ttaagcagat ggataaaaat cttaaactac tgggtgaaag cattaaaaag gcaagaacgc
     1081 ttctgggaat ttctcaggaa gagttagctt ttcgttcaat gttacataga acttatatca
     1141 gctctgtcga aagaggagaa agaaacatta gttttctaaa cctcataaag atagcaaaag
     1201 ctctagaaat ttcaccctct gaactaatag agggaataat atgttaaata atccacatcc
     1261 ttatttaaat aaatcaaaag aagaatggct aaatataaca aatgaattga taaaatcgca
     1321 cccactgact gaaaaagaaa ttgttgacac atgtttgtca gcttgggatg atatgttcaa
     1381 cactgaaatt ggaggtgcta ggttaaaaat agggagagat atattcccaa cacctcaaat
     1441 aataggatac ctattgcacg aacttatccc agccgaaatt gaaaaaaaac acccttcgat
     1501 gtggagaaaa gacgagtcag cacatgagaa agatttggtt tgcctagaaa atgattactt
     1561 ttcaactgaa gtaaaaacat catcaaacaa gaaccaaata tttgggaata gaagctacgc
     1621 tcaagagtca atcagtgata aaaaaagtaa aaatggattt tatataacca taaactttac
     1681 cactccaaag aaagatgtag aagaacccaa agtaaacatc ataaggtttg gttggctaga
     1741 tcatacagat tggattgcgc aaaaggcagc atcagggcag caagcccgac tatcacctga
     1801 tgcttacctt tataaattga aggtgttata taagagctaa aggctctatt cctatttcag
     1861 atttcaactt ataaaactca tctatcctat tagcgattat tttcacataa tcgctattaa
     1921 cttcaaagcc aataaccttt ctaccatttt tcaatgcagc aatggctgtt gtccctgagc
     1981 ccataaacgg gtcgataaca agatcacggt tattactacc cgccttaatt atcctatcga
     2041 tcatttctaa aggaaactgt gcagggtgtt ccgttctttc ctttgaagac ctatttttcc
     2101 ctgatgtaac tttagatatc tgccaaacat ctgatggatt tttccctaaa ggattacact
     2161 tcaacttccc attctttttt tgattagggt atttaacgtt aggatctctg atatcatcca
     2221 gattaaactt atagttatct tggtttttca cataccaaag tatcttttca tttctcggcg
     2281 acaacctttt tttgcatgca acacctgccg aataattcca cactatttct tgtatgagat
     2341 aaaagtcact cttatcccag agaagatacg ggataggaac ggctaatcct ttattttcca
     2401 cttccagata accaacattc aaccagaaag atccatcatc tttagaaatc cgatgtaact
     2461 ctgacatcca gtttgagcac catgatatgt aatcttttag tgcaatgatg ttctcataag
     2521 actttccaat attatatgga ggggatgtca cggcaatatc aaccatgtca gcaggcaatt
     2581 tccgcatagc ctctaaacaa tccatgttat agattagaac atctgtatgt tcatacgctg
     2641 gactgccaag taaagcctta atacgatcaa acatcactca ccttttttat gcttaaatat
     2701 ctataatatg tactacgact aatcccaata tcttcccaag gtttttgaga attaattgaa
     2761 ccaaaactta cgcttccttt gggcctgcca ccaccccggc ttatcttacc tccaacctga
     2821 cctctttttt tcattggagc acctgtgttg ttctgaggtg agcatatcac ctctgttcag
     2881 gtggccaaat tcagtgtgcc acttcaatac ggtcacaccg ttcaagcaga cgctgatgct
     2941 cagtctcggt catgcggatt ttgatcgctt ttgttcgctt ttccataggc tccgcccccc
     3001 tgacaagcat cacagaatcg gacgctcaaa tcagtggtgg cgaaacccga caggactata
     3061 aagataccag gcgtttcccc ctggtggctc cctcgtgcgc tctcctgttc ctgcctttcg
     3121 gtttaccggt gtcattccgc tgttatggcc gcgtttgtct cattccacgc ctgacactca
     3181 gttccgggta ggcagttcgc tccaagctgg actgtatgca cgaacccccc gttcagtccg
     3241 accgctgcgc cttgtccggt aactatcatc ttgagtccaa cccggaaaga cacgacaaag
     3301 cgccactggc agcagccact ggtaactgat ttagaggaga tggacttgaa gtcatgtgcc
     3361 ggttaaggct aaactgaaag gacaagtttt ggtgactgcg ctcctccaag ccagttacct
     3421 cggttcaaag agttgctagc tctgagtacc ttcgaaaaac cgccctgcaa ggcggttttt
     3481 tcgtttgcga caactaatct acgcggtaac cccttatcag gtcaagataa ctatccatca
     3541 gtgcatcttt ccaatacaat ccattaagca acatccctaa agcgtgctcg ctatctattc
     3601 aagtttagcc tgctcaacat tgagcataac caataagtcg aacaggctac ttaccgcttt
     3661 tttgttacta ttcgctgagc gcacacagtc ccacatcatc gaatcgtctg tacaaaaatc
     3721 accacagcag tcagctttaa tattctcgtt aagtagccca agtggtagcc acacataagg
     3781 ctgccccctc aaaatatttg gaacagtcga accacatttt ttgcagaaat cgttacggta
     3841 accactttcc tttttccatg aagaaatcaa ttcctctgag gtttgccagt caaaatcctc
     3901 aactttcact atggtagcta agttatgacc tactccagac tgtcttcggc atagggaaca
     3961 gtggcatcta taaaattttc aggctgattt tttatcgtga atttaacagc accacacaaa
     4021 catgacccac taatcaaaat aatctccatc aaaataaaat acgtatttac cataacatct
     4081 cttgcgtgta ccgcctcaga ggctctcagg gcatttctga cgggaaaccg gtaaaacagg
     4141 caacaaacca cccgaaaacc cgccagaaac gcgcagtctc tgtttttacg gcatgcatga
     4201 atatgcgcgc aagtgcatag cacggaaatt cacgccattc agccggggta agtcctgttt
     4261 ccgatgttct tcttacccga aaacggtgaa cggggacgca atttattgcg tggccgtgag
     4321 gcgttgccgg cgcagccgga aaacccgttt tcatcacgtt caggaagggg ggatgtacaa
     4381 atggcacaga ggatggaagt gacgtatgag ctgaagggat gatgtaaaag tgatgcaaaa
     4441 gtgttgtaaa agtgatgtaa aagtgatgta cagaccgaag gaatgatgca aaagtg
//
