LOCUS       NZ_CP063372             2310 bp    DNA     circular CON 16-JUN-2023
DEFINITION  Escherichia coli strain 1409 plasmid p2.3k, complete sequence.
ACCESSION   NZ_CP063372
VERSION     NZ_CP063372.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN12285857
            Assembly: GCF_014076685.2
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2310)
  AUTHORS   Rhoads,D. and Ekesi,N.S.
  TITLE     Analysis of Genomes of Bacterial Isolates from Lameness Outbreaks in
            Broilers
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2310)
  AUTHORS   Rhoads,D. and Ekesi,N.S.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-OCT-2020) Biological Sciences, BCO Bacterial Genomes,
            1125 W. Maple St, Fayetteville, AR 72701, USA
REFERENCE   3  (bases 1 to 2310)
  AUTHORS   Ekesi,N.S., Alrubaye,A. and Rhoads,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (24-JUL-2020) Biological Sciences, BCO Bacterial Genomes,
            1125 W. Maple St, Fayetteville, AR 72701, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 02-SEP-2020
            Assembly Method :: Ratatosk long read correction, followed
            byUnicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 135.0x
            Sequencing Technology :: Oxford Nanopore MinION; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/16/2023 14:37:40
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,953
            CDSs (total)                      :: 4,835
            Genes (coding)                    :: 4,640
            CDSs (with protein)               :: 4,640
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 195
            CDSs (without protein)            :: 195
            Pseudo Genes (ambiguous residues) :: 0 of 195
            Pseudo Genes (frameshifted)       :: 64 of 195
            Pseudo Genes (incomplete)         :: 123 of 195
            Pseudo Genes (internal stop)      :: 43 of 195
            Pseudo Genes (multiple problems)  :: 37 of 195
            Pseudo Genes (short protein)      :: 5 of 195
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP063372.1.
            Bacteria and source DNA available from Douglas Rhoads, 601 SCEN,
            850 W. Dickson St, Biological Sciences, University of Arkansas,
            Fayetteville, AR USA 72701.
            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..2310
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="1409"
                     /isolation_source="leg bone from commercial broiler"
                     /host="Gallus gallus"
                     /db_xref="taxon:562"
                     /plasmid="p2.3k"
                     /geo_loc_name="USA: Arkansas commercial broiler farm"
                     /collection_date="2016-07-22"
                     /collected_by="Nnamdi Ekesi"
                     /identified_by="Nnamdi Ekesi"
     gene            join(1958..2310,1..145)
                     /locus_tag="FOI11_RS24440"
                     /old_locus_tag="FOI11_024440"
     CDS             join(1958..2310,1..145)
                     /locus_tag="FOI11_RS24440"
                     /old_locus_tag="FOI11_024440"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001027759.1"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA];
                     GO:0006276 - plasmid maintenance [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="WP_001027759.1"
                     /translation="MNITERTDSKKKVLRQNITEVIDRETGNITQEITDITVQFPQEPA
                     YVKIYIDNLCAVTKAPDSLKDVLFLILRKLDYDGYIALSTRYRKEICKLLGIKDGTLRN
                     RLYSLSKMGIIASCGGNEYQANPNLFARGEWKKIIEQRREFEMRIKYSPNGETIITTEE
                     IK"
                     /name="replication/maintenance protein RepL"
     gene            complement(179..604)
                     /gene="mobA"
                     /locus_tag="FOI11_RS24445"
                     /old_locus_tag="FOI11_024445"
     CDS             complement(179..604)
                     /gene="mobA"
                     /locus_tag="FOI11_RS24445"
                     /old_locus_tag="FOI11_024445"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001107325.1"
                     /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_001107325.1"
                     /translation="MAKNKRSGSEVRQRTKVITLRVNNRVASEIRRRAKNEGLTISEYI
                     RTASLNNEIKQRVPSRYLDELIRLGRMQKKLFDKGKRPKDKEYLEVMHKIILLCDEMKI
                     VTKRISDVYNEMDLIKDEIKIIKRIHKNKYPGSDLFK"
                     /name="mobA"
     Typing          complement(1351..1609)
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.415"
                     /coverage="100.0"
                     /evalue="6.900000000000001e-74"
ORIGIN
        1 tggcggtaat gaatatcagg cgaaccctaa tttatttgct cgtggtgaat ggaaaaaaat
       61 aattgaacag cgtcgcgagt ttgaaatgag aattaaatat tcacctaacg gtgaaactat
      121 tataacaacc gaagaaataa aataatgtgc acctaaataa ggtcttttta aaaagacctt
      181 atttgaataa atccgaacct ggatatttat ttttatgtat cctttttatt atttttattt
      241 catcctttat taaatccatt tcattatata catcagaaat tcgcttcgtt actattttca
      301 tttcatcgca aagtaaaatt attttatgca tcacctcgag gtactcctta tccttcggcc
      361 gctttccctt atcaaataat ttcttctgca tccgaccaag tcggattaat tcatctaaat
      421 acctggaagg tacgcgctgt tttatttcat tatttaaact tgccgtcctg atatattctg
      481 aaattgtcag tccttcgttc ttcgctcgcc gtctgatttc gcttgcgact ctgttattta
      541 ctctaagggt gataacctta gttctctgcc gtacttctga accactacgt ttatttttag
      601 ccatcgcaat gactctccat tttgcacgtt tggggtgtcg gggcttgccc tgacaggagg
      661 tattctcatg caagcgaatg tattcgcggt atgacgaata cacatcctgt ccagttttcc
      721 gctacaactt ttcgacgaaa ataaaatacc gcgtcgtaac ctggtatttc tgatacaaaa
      781 aaatgatgct tcattcaata ttatttacac agattttaaa aattattgct tgttatttaa
      841 taaataacat cgaattaatt gatgtctttg ttgtctgtcg tttgtggatt attggaggga
      901 taaagattag atcttcctcg ttatataatc cattgcctgt taatgatacg gagtgtgtcc
      961 aaggaacagg aagcggaaga gcaagatagt agcatgtaca taaaatataa atccgtgagt
     1021 tattgatatc gcgtttatat attaaaaata taacttaaca ttgctcttaa tatttatttt
     1081 gtcctggcaa tgggagcatt aatccccgtg cagtgctccg ccagctgctg acaacctcga
     1141 catataacca tcgatacgat agaacatcag ggcgcgtttc cggcaagaac taaccatggg
     1201 gatggtttgc gtgccgacaa acgccggaac gcgcctcaaa tccaccaagc caccacggtt
     1261 ccggcagcgc cttgagcgca accggaaacc gtctggggag aaccccagac ccccaccgct
     1321 gcaacatcat cggtctacga ccacctacca accgagtggc tacctgtgcc gtgcgaacag
     1381 gctttgcagg gggctggcgc ggttcctggc gacctgaaag cccctggtta ggggtatcgg
     1441 cgcgcctggc ctcctgaaac cctctgtaag cgtttttcgc gcctttcatg ccctgacggg
     1501 catttaaacc ccgtttcgtg cgtctgggag gctctgagcg cgtttaacag atgaccagcg
     1561 actcgatcgc ctgagatcaa atcgggatca tcaacgatat gcgagaggtg gcaccgctcg
     1621 ccgcagcccc agcgaccgaa cgtagtgagc gagtgggcga ggaagcggaa gagaaccgga
     1681 agctacattg agcacgcacg ctcaatatta aaattgtcac ttcgtaatat agagattatg
     1741 cctcgtgctt atggatacat ttaaaaatat aagatatccg aattaggcta catacgggct
     1801 gatcgccaat gttgtaacgt gtagaagata cacctgtaac gtgtacagga tactcctgta
     1861 acgtgtgggc ggtattgtcg taatctatat tgagtgacat tttgtttttt tggcattata
     1921 ttgtctgtca cctttataaa gtgacaaagg cgataaaatg aacattactg aaagaacgga
     1981 tagcaagaaa aaagttttaa gacaaaatat tactgaggtt atagatagag aaactggaaa
     2041 cataacacaa gaaataaccg atataacagt tcaatttcca caagaacctg cgtatgtgaa
     2101 aatttatatt gataatttat gtgctgtcac aaaagcacct gattctctaa aagatgtttt
     2161 atttttaatt cttaggaaat tggattatga cggatatatt gcattatcaa ctagataccg
     2221 taaggagatc tgtaaattat tgggaataaa agacggaaca ttacgtaaca gattgtattc
     2281 attatcaaaa atggggatta ttgctagttg
//
