LOCUS       NZ_CP104545             4593 bp    DNA     circular CON 07-OCT-2023
DEFINITION  Escherichia coli strain E6 plasmid p6, complete sequence.
ACCESSION   NZ_CP104545
VERSION     NZ_CP104545.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN30789309
            Assembly: GCF_025369915.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4593)
  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  JOURNAL   Unpublished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 4593)
  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 07:35:50
            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)                     :: 5,147
            CDSs (total)                      :: 5,028
            Genes (coding)                    :: 4,836
            CDSs (with protein)               :: 4,836
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 192
            CDSs (without protein)            :: 192
            Pseudo Genes (ambiguous residues) :: 0 of 192
            Pseudo Genes (frameshifted)       :: 82 of 192
            Pseudo Genes (incomplete)         :: 113 of 192
            Pseudo Genes (internal stop)      :: 37 of 192
            Pseudo Genes (multiple problems)  :: 39 of 192
            Pseudo Genes (short protein)      :: 2 of 192
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP104545.1.
            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..4593
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="E6"
                     /isolation_source="Broiler"
                     /host="Poultry"
                     /db_xref="taxon:562"
                     /plasmid="p6"
                     /geo_loc_name="USA"
                     /collection_date="2017-06-02"
                     /collected_by="USDA"
     gene            complement(193..1032)
                     /locus_tag="N5O76_RS25595"
                     /old_locus_tag="N5O76_25595"
     CDS             complement(193..1032)
                     /locus_tag="N5O76_RS25595"
                     /old_locus_tag="N5O76_25595"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354646.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001354646.1"
                     /translation="MLTLFIFFVLLIAACFFCFAPPRRGYDRNEIIPYKIKLSINKYRL
                     YIYSSGKVRQYLLFLVILSLYYSIAEPFKSELIKNISYSLMAAFIFDTGLNFSKENITK
                     GVISTRWHNDLYSSFERMKAINKIYYPSNKEINTEGLSKAITSSLFNDDANSFAKRDFR
                     LMWDLSSEKYLSYKEIIIRKGDKLDAVCLRFINDDYKFLVNFNRDEEVFKYFPSIMQPS
                     LKTYRALSRLVNSIKDPSRFKFTTESLEMELLEYLELRNELFNDIEEVMGSYAQRAP"
                     /name="hypothetical protein"
     gene            complement(1224..1373)
                     /locus_tag="N5O76_RS25795"
     CDS             complement(1224..1373)
                     /locus_tag="N5O76_RS25795"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001326446.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032194431.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPERHVKTPLAAAIGNRLEELVLK
                     LCAG"
                     /name="hypothetical protein"
     gene            complement(2043..2234)
                     /locus_tag="N5O76_RS25600"
                     /old_locus_tag="N5O76_25600"
     CDS             complement(2043..2234)
                     /locus_tag="N5O76_RS25600"
                     /old_locus_tag="N5O76_25600"
                     /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_000165986.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2297..2620
                     /locus_tag="N5O76_RS25605"
                     /old_locus_tag="N5O76_25605"
     CDS             2297..2620
                     /locus_tag="N5O76_RS25605"
                     /old_locus_tag="N5O76_25605"
                     /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_001677263.1"
                     /translation="MLTIRVSDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGHWSSIDRVHVVAALMAIEGELRQLRQAVREQGGR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2829..>3263
                     /locus_tag="N5O76_RS25610"
                     /old_locus_tag="N5O76_25610"
                     /pseudo=""
     CDS             2829..>3263
                     /locus_tag="N5O76_RS25610"
                     /old_locus_tag="N5O76_25610"
                     /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            3298..3858
                     /locus_tag="N5O76_RS25615"
                     /old_locus_tag="N5O76_25615"
     CDS             3298..3858
                     /locus_tag="N5O76_RS25615"
                     /old_locus_tag="N5O76_25615"
                     /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_000067488.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKQQLDTLSTTVSTQLSTTEAELSRQQKNLLWQVIKGRVLFPALTA
                     LSVTGGIFLGCWGLIQWQESRIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            3865..4098
                     /locus_tag="N5O76_RS25620"
                     /old_locus_tag="N5O76_25620"
     CDS             3865..4098
                     /locus_tag="N5O76_RS25620"
                     /old_locus_tag="N5O76_25620"
                     /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_000137388.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHAVTQQNNA
                     ILNERVVNLSQQVQLLAGQVDRLSRLFITNNR"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          1871..1955
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.03e-37"
     Typing          complement(1302..1860)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.761"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2611..4196
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.811"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 caatcgtatt gcgcaccatg aacctattct caaccgcaat ctggaggatg attttgctac
       61 gataaagaga attatcgcgt atcggtgtca gcattcattg gagtggatgc tgaaaaacca
      121 ggtgttactc cctctactta cacttaaacc tctctaaaaa tataagtaag tactatcgag
      181 ggctatcatg aactatggtg ccctctgagc atagctaccc attacttctt ctatgtcatt
      241 gaataattca tttcttaact ctaagtattc tagtaactcc atttctaatg actctgtcgt
      301 gaacttaaat ctagaaggat ctttgattga gtttactagt cttgataacg ctctatatgt
      361 tttgagtgaa ggttgcatta tagatggaaa gtatttgaaa acctcttcat ctctgttgaa
      421 attaactaaa aacttgtagt catcatttat aaatctcaag catacagcgt caagcttatc
      481 gccttttctt attattattt ctttatagga aagatatttt tcagaagata agtcccacat
      541 caagcgaaaa tctctctttg cgaacgagtt cgcgtcatca ttgaaaagag atgatgtgat
      601 ggctttggat agaccttctg tgtttatctc tttgttggat gggtagtaaa ttttattaat
      661 tgctttcatt ctctcaaatg atgaatatag gtcattatgc caccttgttg aaatcactcc
      721 tttagttata ttctccttgc taaaattaag ccctgtatca aaaataaatg cagccatcag
      781 tgaatatgat atgtttttta ttaactcaga cttaaatggt tccgctatgg agtagtacag
      841 tgataaaata actaaaaata aaaggtattg tcttaccttt cccgatgagt atatgtaaag
      901 gcgatattta tttattgata gttttatttt gtatggaatg atctcatttc tgtcatatcc
      961 tcttcgtggt ggagcaaaac aaaagaaaca tgcagctatt aataaaacaa aaaagatgaa
     1021 cagtgtaagc aagttcggct cctgtgtatg ctcactatgc atgattgtct tgagatctaa
     1081 cgatcctgaa ggtagtcttg tccgtaaacg aaaaaaccgc ccagcaaggc ggcttttcga
     1141 aggttctcag agcagcaact ctttgaacca aggtaactgg cttggaggag cacagccacc
     1201 aaatctgtcc tttcagttta gccttaaccg gcgcataact tcaagactaa ctcctctaaa
     1261 cggttaccaa tggctgctgc cagtggcgtt tttacgtgtc tttccgggtt ggactcaaga
     1321 cgatagttac cggataaggc gcagcggtcg ggctgaacgg ggggttcgtg cacacagccc
     1381 agcttggagc gaacgaccta caccgggccg agataccaac agcgtgagct atgagaaagc
     1441 gccacgcttc ccgaagggag aaaggcggac aggtatccgg taagcggcag ggtcggaaca
     1501 ggagagcgca cgagggagct tccaggggga aacgcctggt atctttatag tcctgtcggg
     1561 tttcgccacc tctgacttga gcatctgttt ttgtgatgct cgtcaggggg gcggagccta
     1621 tggaaaaacg ccagcggcgc ggccttcttc ctgttcctgg ccttttgctc acatgtttct
     1681 tttggcgtta tcccctgatt ctgtggataa ccgcatcacc gtctttgagt gagctgatac
     1741 cgctcgccgc agccgaacga ccgagcgtag cgagtcagtg agcgaggaag cggaagagcg
     1801 cctgatgcgg cattttctcc ttacgcatct gtgcggtatt tcacaccgca tatggtgcac
     1861 ttttcttata atccgcactg atgccacata gttaagccag tatacactcc gctatcgcta
     1921 cgtgactggg tcagggctgc gccccgacac ccgctaaaac ccgctgacgc gccctgacgg
     1981 gcttgtctgc tcccggcatc cgctcacagg caagctgtga acgtctccgg gagctgcatg
     2041 tttcagttgc tttcaccgtc atcgccgaag cgtgcgaggc aactacggta gagttcgtcg
     2101 gcgtggtcgt gaagtgattc gcagatgtct gcctgttcgt ccgcgtccag ctcgttgagt
     2161 ttttccagca gggtcagcgt ctggcttctg ataaagcggg ccatgttaag ggctgttttt
     2221 tcctgtttgg tcatggtctt aaggctcctt aataggggat tttttagggg gaatgatacc
     2281 gatgaaacgc gagaagatgc tcacgatacg ggttagcgat gaggagcacg cccggttact
     2341 ggaacgctgc gagggtaaac gactggcaga atggatgcgg cgggtctgtc tgggggagcc
     2401 ggttgcgcgc acaggaaaac tgccgacact atcgccgcca ttgctgcggc atctggctgc
     2461 catcgggaac aatctgaacc agacagcccg gaaggtgaac agcggccact ggtcttcgat
     2521 tgaccgggtt catgtggtgg ccgctctgat ggccatcgag ggtgaattgc gccagttgcg
     2581 gcaggctgtc agggaacagg ggggacggga tgatagttaa atttcatgcc agggggaaag
     2641 gcggtggaag tggcccggtc gattacctgc tggggcggga gcgtaaccgc gaaggcgcaa
     2701 cggtgctccg gggtaacccg gaagaaatcc gggaactcat tgatgccacg ccattttcga
     2761 agaaatacac gtcaggcgtt ctgtcgttcg cggagaagga gttaccgccg ggtgaacgcg
     2821 aaagagtgat gacgagcttt gagcgtgttc ttatgcccgg tctcgaaaaa aaccagtaca
     2881 gcattctctg ggtggaacac caggataagg ggcggctcga actgaatttt gtcattccga
     2941 acatggaact acagagcggt aagcgcctcc agccgtacta cgaccgtgcg gacaggccga
     3001 ggataaatgc ctggcagacg ctggttaatc atcattacgg gctgcgtgac ccgaacgcac
     3061 cggagaacag acggacgctt gtcacaccga ataatctgcc aaaagcgaaa caggaggccg
     3121 cagaagcgat tacacggggt cttgaggcgc tttaccgtgc cggagcaata aaaacgcgtc
     3181 aggatgtcac tgaggcgctc acagcggcag gttttgaggt ggtgaggaca accagaagca
     3241 gtatcagtat tgccgacccg gagggggggc ggaatctcag gctaaagggg gcgctgtatg
     3301 agcaatcttt tacaaatggg aacggacttc gagaagaaac tgaaagagcg agccgcttct
     3361 accgagaaca tgctgaacag cgagttcagg aagctagaag agtctgtaga caaggcactg
     3421 agcttaaaca ggcagaaaat cagagacgct atcagcgaac atacaacatc cgtgaaacag
     3481 caactggata cgctgagcac caccgtgagc acgcagctca gcaccacaga ggccgaactg
     3541 tcccggcagc agaaaaacct gctctggcag gtgatcaaag ggcgggtact gtttccggcg
     3601 ctgaccgcgc tcagcgtcac gggcggcatt ttcctggggt gctgggggct gattcagtgg
     3661 caggaaagca ggattgcgaa aaatatcttg accatcagag agcaggaaaa cacgctggcg
     3721 aaactcgagg caaaaacctg gggggtgacg ttcgtcaatg gcgagaacgg gaaatttctg
     3781 gtgctgccgg acggggtgaa aggggaaaac acctggacgg tgggcgacaa gaacgccgtg
     3841 aggctggtca gggagtaaac gagtatgacg gaactggaag ggcatttgct gaacgcctta
     3901 gagcatttgc aacaggacta tatgcggcgg ctgaacgagt gggagagcgc cttcgcagaa
     3961 ttgcagaaga tgcacgcggt tacgcaacag aacaacgcga tactgaacga gcgtgtcgtg
     4021 aacttgagtc agcaggtgca gctattagcc ggacaagtcg accgcttgag tcggttattt
     4081 atcacgaaca acagataagg gatgaacagg agcgtcaggc gcaggagctt gcccggcgct
     4141 ggcatgaaga gcaggaaccc gaagcgcgga tctggcgtgg cccgtcaatg gggatgtgac
     4201 cggggtaccc cctgaaatcg agccagtttg tggcacgccc tacccggatg gcgccaatgt
     4261 taatgtacgt acattagcat taacaatatc caaacctccc cattttgccc cgttcgacgg
     4321 ctggaacgtg cgaaactgat cgtcattcag tttcgcgcat aactatgcat gaggttaaaa
     4381 tttaccaggc gcgatcgcgg cagtttttcg ggtggtttgt tgctgttttt acctgtctgc
     4441 tgccgtgatc gcgctgaacg cgtttaagcg gtacgcgcaa tgcgacgtta tggtaaatac
     4501 ggagtatttt aattgcgggc ctttgttgta tatctctgtc gtttgtcccc ggggggaagc
     4561 attactgcta acaagtcccg tgagaaaact gcg
//
