LOCUS       NZ_CP135962             1552 bp    DNA     circular CON 01-NOV-2023
DEFINITION  Escherichia coli strain MS1266 plasmid pAPEC-O2-MS1266-3, complete
            sequence.
ACCESSION   NZ_CP135962
VERSION     NZ_CP135962.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN37560771
            Assembly: GCF_033098885.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1552)
  AUTHORS   Jia,L., Devkota,P., Arick,M.A. II, Hsu,C.-Y., Peterson,D.G.,
            Evans,J.D., Sukumaran,A.T. and Zhang,L.
  TITLE     Complete genome sequences of two avian pathogenic Escherichia coli
            strains isolated from broilers exhibiting colibacillosis in
            Mississippi
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1552)
  AUTHORS   Jia,L., Devkota,P., Arick,M.A. II, Hsu,C.-Y., Peterson,D.G.,
            Evans,J.D., Sukumaran,A.T. and Zhang,L.
  TITLE     Direct Submission
  JOURNAL   Submitted (27-SEP-2023) Poultry Science, Mississippi State
            University, 46 Old Bully Blvd, 100 Hill Poultry Science Building,
            Mississippi State, Mississippi 39762, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Flye v. 2.9; Unicycler v. 0.5.0
            Assembly Name                     :: MS1266
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 602.4x
            Sequencing Technology :: Illumina HiSeq; Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/01/2023 10:18:32
            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)                     :: 4,816
            CDSs (total)                      :: 4,702
            Genes (coding)                    :: 4,570
            CDSs (with protein)               :: 4,570
            Genes (RNA)                       :: 114
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 132
            CDSs (without protein)            :: 132
            Pseudo Genes (ambiguous residues) :: 0 of 132
            Pseudo Genes (frameshifted)       :: 55 of 132
            Pseudo Genes (incomplete)         :: 93 of 132
            Pseudo Genes (internal stop)      :: 18 of 132
            Pseudo Genes (multiple problems)  :: 32 of 132
            Pseudo Genes (short protein)      :: 3 of 132
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP135962.1.
            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..1552
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="MS1266"
                     /isolation_source="Chicken spleen (Gallus gallus)"
                     /host="Gallus gallus"
                     /db_xref="taxon:562"
                     /plasmid="pAPEC-O2-MS1266-3"
                     /geo_loc_name="USA:Mississippi"
                     /lat_lon="33.4504 N 88.8184 W"
                     /collection_date="2019-03-21"
                     /collected_by="Mississippi State University Department of
                     Poultry Science"
     gene            complement(667..1143)
                     /locus_tag="RTE58_RS24080"
                     /old_locus_tag="RTE58_24085"
     CDS             complement(667..1143)
                     /locus_tag="RTE58_RS24080"
                     /old_locus_tag="RTE58_24085"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000469298.1"
                     /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 domain-containing protein"
                     /protein_id="WP_000469298.1"
                     /translation="MFIDSEKRLKQLSDEAKKNTEDLEEAKKNSRFTQVSPKGWERVRE
                     LLKDSQGISALKLYSFLAEHIDPTCGAVVADQQFLAEKLGVSRSTIIRWLNYLESKNAL
                     VRIPVAGKVCAYALDPHEVWKGYNTTKNHAAFVTKTLVNKDGDIQRRIMAMFSN"
                     /name="helix-turn-helix domain-containing protein"
     Typing          1223..1331
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.95e-50"
     Typing          177..437
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.511"
                     /coverage="100.0"
                     /evalue="3.95e-106"
ORIGIN
        1 atgtgcaaat gtaataccgt cacccgcgac gatattccgt ttgccatctg gtcagggctt
       61 caccccgaca ccccgcatca gtgcgtacgt gctcaatgtg gtttccggtt ctcttccgct
      121 tcctcgccca ctcgctcact aacgttcggt cgctggggct gcggcgagcg gtgccacctc
      181 tcgcatgttg tcggtgattc cgctgttgtt ctttcgggga tgagtcgtca gatagccctt
      241 caaacgcgct cagaagctct cagacgcacg aggcggggtt taaatgcccg tcagggcatg
      301 gaaggcgcga aaaacgctta cagagcgttt caggaggtca ggcgcgccga tacccctagc
      361 caggggcttt caggtcgcca ggaaccgcgc cagccccctg caaagcccat ttgcacggta
      421 caggcagtca ctcggttggt aggtggtcgt agaccgtcgg tgttacagcg atgggggtct
      481 ggggttctcc ccagacggtt tccggttgcg ctcaaggcgc tgccggaacc gtggcggctc
      541 ggtcgttctg gagatcgggg agcaaaaaca cgcaagggat tttgaggcgg caaaagagca
      601 atgcaggata gacaatcatg gtcagaacgt taacacgtag cccctgattg tccgcctgcc
      661 gctggctcaa tttgaaaaca tggccatgat tcggcgctga atatcaccgt ctttgttgac
      721 cagtgtttta gtgacaaatg ctgcatggtt tttcgtagtg ttgtatccct tccagacttc
      781 atgtggatcg agggcatacg cacaaacctt accagcaacg gggattctaa ctaatgcatt
      841 ttttgattct aagtaattga gccaacgaat aattgtgctt ctgctaactc caagtttttc
      901 agctaggaat tgctgatccg caacgacagc gccacacgta ggatcgatat gctccgctaa
      961 aaatgagtac agcttcagtg ctgatatgcc ttggctatcc ttcagcagct ctcgaacgcg
     1021 ttcccaacct tttggggata cctgtgtaaa ccttgaattc ttctttgctt cttcgagatc
     1081 ctcggtgttt ttctttgcct catctgaaag ttgtttcagt cgtttttctg aatcaataaa
     1141 catgattttt tccctctaaa aatcccatgc actaacgttg gttcaaatct aagccatcat
     1201 gacacatctg tgcaacacct tgttgcgtgt tgtcgcatcc tggatgcgac aacgttgtgt
     1261 caccctggat gcgacaggta aacaaaaaac acactaaaaa aacaacaact tacaaatcgg
     1321 cgtaaaagat ctattctagg caagggtgtt gcgcgcaacg caacgccctt tgggggtgtc
     1381 ggggcgaagc cctgacccag tcacgtagcg atagcggagt gtatactggc ttaatcctct
     1441 gcaagcctcg tcagccgtga tttttgccag atttcgaggt tttcacgttc aacagctcct
     1501 gcacgttttt tgccgtccgt tcaccgttaa actccgcaga aatcgggaca gg
//
