LOCUS       NZ_AP026787             2756 bp    DNA     circular CON 27-NOV-2023
DEFINITION  Escherichia coli strain IPCEC31 plasmid pIPCEC31_4, complete
            sequence.
ACCESSION   NZ_AP026787
VERSION     NZ_AP026787.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00533653
            Sequence Read Archive: DRR403237, DRR403240
            Assembly: GCF_026001065.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1
  AUTHORS   Suzuki,M., Tran,H.H. and Shibayama,K.
  TITLE     Complete genome sequence of Escherichia coli IPCEC31
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2756)
  AUTHORS   Suzuki,M., Tran,H.H. and Shibayama,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-SEP-2022) Contact:Masato Suzuki National Institute of
            Infectious Diseases, Antimicrobial Resistance Research Center; 4-2-1
            Aobacho, Higashimurayama, Tokyo 189-0002, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8.0
            Genome Coverage                   :: 236x
            Sequencing Technology             :: Illumina MiSeq; ONT MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/27/2023 03:11:06
            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)                     :: 4,943
            CDSs (total)                      :: 4,825
            Genes (coding)                    :: 4,560
            CDSs (with protein)               :: 4,560
            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)              :: 265
            CDSs (without protein)            :: 265
            Pseudo Genes (ambiguous residues) :: 0 of 265
            Pseudo Genes (frameshifted)       :: 76 of 265
            Pseudo Genes (incomplete)         :: 182 of 265
            Pseudo Genes (internal stop)      :: 40 of 265
            Pseudo Genes (multiple problems)  :: 32 of 265
            Pseudo Genes (short protein)      :: 4 of 265
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP026787.1.
            Annotated by DFAST https://dfast.ddbj.nig.ac.jp/
            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..2756
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="IPCEC31"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pIPCEC31_4"
                     /geo_loc_name="Cambodia:Phnom Penh"
                     /collection_date="2016"
     gene            complement(579..1856)
                     /locus_tag="OO978_RS24590"
                     /old_locus_tag="IPCEC31_47340"
     CDS             complement(579..1856)
                     /locus_tag="OO978_RS24590"
                     /old_locus_tag="IPCEC31_47340"
                     /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="plasmid recombination protein"
                     /protein_id="WP_264824786.1"
                     /translation="MKSQFMHVELYSREEPAKKTINKSKNINHKSDVRTTTVNGVLSEM
                     KREEGFTSHLEAIAAPEVLYGSISDLERSIERYEAEFKTTDKNGKEKKLRKDACILLAG
                     VVSLDRADEDIWDEYKTKSIEYLKNKYGENLKCVVEHTDETNPHFHFYVVGNKDQDLNL
                     LHDGKLAVSKLAKEDKKKLHQTVYTEAMIKFQDDFYTKVSNKFGLSRTGEEPRERYKSR
                     PEYLRFKKRQETALNILSDIEEFEADIKEKARKTGYSKGAKQFQNKTWVIKVGEAIKLL
                     GKEHKAELDQKEKELEKIKKEKTEIETELNLKKEELSNAYSQRNEASRKNSVYIDKVNA
                     LKKENKLLLPYKDQFDLKLQQEKEPLQAEVKELTSENNNLKNENSELKKENLDFKEFIL
                     GVKNYYGSKFDEWCKEIFKTKTKYKY"
                     /name="plasmid recombination protein"
     gene            complement(2100..2699)
                     /locus_tag="OO978_RS24595"
                     /old_locus_tag="IPCEC31_47350"
     CDS             complement(2100..2699)
                     /locus_tag="OO978_RS24595"
                     /old_locus_tag="IPCEC31_47350"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_019704520.1"
                     /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_264824784.1"
                     /translation="MAKAKVLINDTDEAVIKNALDVEDMNEVNINVTRKKKTGFLGTYS
                     IVFHDSVKTLSKMNLKPNAYKIVMYLFGIIEMGNILVNFSQKKIADDLGLQPSNVSRAF
                     KELFDKGVLIKDSEDGHVYLNSNLCTMGVPKNFDQKRMKSLQKSNIETEDFKNQINLFT
                     PTNTTKIKTNDKKVIKKETKENVLEFPMQNDWVDIE"
                     /name="helix-turn-helix domain-containing protein"
ORIGIN
        1 agtgcaatgt caatatcaaa acgataactt tcttatcgtt ttaacatcaa atcatatcaa
       61 tgcacctgta tgcaaaatta tgattttcat aagtccgatt atgattttca taattttgca
      121 ttatgatttt cataattgaa aattatgatt ttcataattt tttttttggt aaagtgttga
      181 tatataaggg tttaaagggt gcttaagaag taagaaaata agaaagaaga aaccgtaaaa
      241 accgccctcg ccgggctggg ccaacccctc gaaccacaga accacaagtg gttctgcagt
      301 tctcacggtt tatagtttta aagggggaac ccctaaaccc gttccccccg cagacaagag
      361 tacttgtctg gcccccccac cccatgcggt caagatcctt gcccacattt tacccacttt
      421 aatttttatc atttaagtta ttgatttata taaatttaca actgcgtgca aaaccatttt
      481 tttgggataa atcccagcta tgacagctaa acgctgtcag gccgctttta gtggtgtctc
      541 atacaccaca tgggcggcag atatgaatat atttcagatt agtatttgta ttttgtcttt
      601 gttttgaata tttctttaca ccattcatca aatttagatc catagtaatt tttaacaccc
      661 aaaataaatt ctttgaaatc taaattttct tttttcagtt ctgaattctc atttttcaaa
      721 ttgttatttt cagaagtcaa ctctttgact tctgcttgta atggctcttt ttcttgctgt
      781 aatttcaaat caaattgatc tttatatggt agcaatagtt tattttcttt ttttagagcg
      841 tttactttat caatataaac gctgtttttt ctcgatgctt catttctttg actataggca
      901 ttagataatt cttctttttt caaattaagc tcagtttcaa tttctgtttt ttcttttttt
      961 attttttcta actctttttc tttttggtct aattctgctt tatgctcttt tccaagtaat
     1021 ttaattgcct caccaacctt aattacccat gttttatttt gaaattgttt tgcaccttta
     1081 ctatatcccg ttttccttgc cttttcttta atatcagctt caaattcttc tatatcagat
     1141 aatatattta atgctgtttc ctgccttttt ttaaatctca aatattccgg gcgggatttg
     1201 tagcgttctc gcggttcctc gcccgttctg ctcaatccaa atttattaga taccttggta
     1261 taaaaatcat cttgaaattt aatcatggct tctgtgtaaa ctgtttggtg caattttttc
     1321 ttgtcttctt ttgctaattt agatactgct aattttccat catggagcaa atttaaatct
     1381 tgatccttgt ttccaacaac gtaaaaatga aaatgtgggt ttgtttcatc tgtatgctca
     1441 acaacacatt ttaaattttc accatattta tttttcaaat attcaattga ttttgtctta
     1501 tattcatccc aaatatcttc atcagctcga tctagagaaa caaccccagc aagtaaaatg
     1561 catgcatctt tgcgtagctt cttctccttg ccgtttttat cagtagtctt aaattcagcc
     1621 tcgtaacgct ctatagagcg ttctagatcg cttatagagc catagagcac ctccggtgca
     1681 gctatggctt ctaaatgaga tgtaaaacct tcctcccttt tcatttctga caacacaccg
     1741 tttacggttg ttgttctaac atcagattta tgatttatat ttttactttt atttattgtc
     1801 ttttttgctg gttcttctct gctgtagagt tctacatgca taaactgtga tttcattttt
     1861 tattctccta tatttttgct ttccttatta tgttaattaa cacctatggt ttttctgtca
     1921 atagctatag gaaccgacta tatctattac actgtcatat ttcatatgac gttccataga
     1981 tgcggctctc cgagggtaaa accaaaatca acaccaaaaa gaaaatcccc aaacattata
     2041 aatctatgat ttatgatgtt tagggattca gcaagcgaag cgcggtagct ttagttttac
     2101 tattcaatat ctacccaatc attttgcata ggaaactcta acacattttc tttagtttct
     2161 ttcttgataa ctttcttatc attagttttt atttttgttg tgtttgttgg agtaaacaaa
     2221 ttgatctgat ttttaaaatc ttcagtttca atatttgatt tttgtaagct tttcattctc
     2281 ttttgatcaa agtttttcgg aacacccata gtgcatagat ttgaatttaa gtaaacgtgt
     2341 ccgtcttcgc tatctttgat taaaacccct ttatcaaaaa gctctttgaa agctcttgat
     2401 acattagacg gctgtaagcc cagatcatca gctatctttt tttgtgagaa gttaactaaa
     2461 atattaccca tttctattat gccaaaaaga tacataacta ttttgtaagc attaggcttt
     2521 aaattcattt tagagagtgt ttttacagaa tcatgaaaaa ctattgaata agtccctaaa
     2581 aatccagttt tcttttttct cgtgacgtta atatttactt cgttcatatc ttcaacatct
     2641 aatgcgtttt ttattactgc ttcatctgta tcgtttatta aaacttttgc ttttgccatt
     2701 ttatattcct ttttctaata aaaataataa cctatgttgc atttataacc gatcta
//
