LOCUS       NZ_CP056078             1552 bp    DNA     circular CON 17-JUN-2023
DEFINITION  Escherichia coli strain MS1170 plasmid pMS1170_3, complete sequence.
ACCESSION   NZ_CP056078
VERSION     NZ_CP056078.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14503865
            Assembly: GCF_016767775.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1552)
  AUTHORS   Li,T., Castaneda,C.D., Arick,M.A. 2nd, Hsu,C.Y., Kiess,A.S. and
            Zhang,L.
  TITLE     Complete genome sequence of multidrug-resistant avian pathogenic
            Escherichia coli strain APEC-O2-MS1170
  JOURNAL   J Glob Antimicrob Resist 23, 401-403 (2020)
   PUBMED   33246209
REFERENCE   2  (bases 1 to 1552)
  AUTHORS   Li,T., Castaneda,C., Arick,M.A. II, Hsu,C.-Y., Kiess,A. and Zhang,L.
  TITLE     Direct Submission
  JOURNAL   Submitted (22-JUN-2020) Institute for Genomics, Biocomputing &
            Biotechnology, Mississippi State University, 650 Stone Blvd.,
            Mississippi State, MS 39759, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Canu v. 1.9
            Assembly Name                     :: IGBB_E1170_1.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 514.0x
            Sequencing Technology :: Oxford Nanopore GridION; Illumina HiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/16/2023 19:59:45
            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)                     :: 4,819
            CDSs (total)                      :: 4,705
            Genes (coding)                    :: 4,568
            CDSs (with protein)               :: 4,568
            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)              :: 137
            CDSs (without protein)            :: 137
            Pseudo Genes (ambiguous residues) :: 0 of 137
            Pseudo Genes (frameshifted)       :: 62 of 137
            Pseudo Genes (incomplete)         :: 87 of 137
            Pseudo Genes (internal stop)      :: 20 of 137
            Pseudo Genes (multiple problems)  :: 30 of 137
            Pseudo Genes (short protein)      :: 3 of 137
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP056078.1.
            Bacteria and source DNA available from Dr. Zhang's Lab, Department
            of Poultry Science, Mississippi State University, P.O. Box 9665
            Mississippi State, MS 39762.
            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="MS1170"
                     /isolation_source="yolk sac"
                     /host="Gallus gallus"
                     /db_xref="taxon:562"
                     /plasmid="pMS1170_3"
                     /geo_loc_name="USA:Mississippi"
                     /lat_lon="33.45 N 88.81 W"
                     /collection_date="2019-03-07"
                     /collected_by="Mississippi State University Department of
                     Poultry Science"
     gene            complement(667..1143)
                     /locus_tag="HED12_RS23140"
                     /old_locus_tag="HED12_23140"
     CDS             complement(667..1143)
                     /locus_tag="HED12_RS23140"
                     /old_locus_tag="HED12_23140"
                     /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
//
