LOCUS       NZ_CP095158             2348 bp    DNA     circular CON 03-JUN-2024
DEFINITION  Escherichia coli strain Iso00041 plasmid pIso00041_03, complete
            sequence.
ACCESSION   NZ_CP095158
VERSION     NZ_CP095158.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17766542
            Assembly: GCF_022964895.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2348)
  AUTHORS   Pankok,F., Taudien,S., Dekker,D., Thye,T., Oppong,K., Akenten,C.W.,
            Lamshoeft,M., Jaeger,A., Kaase,M., Scheithauer,S., Tanida,K.,
            Frickmann,H., May,J. and Loderstaedt,U.
  TITLE     Microepidemiology of plasmids in Escherichia coli and Klebsiella
            pneumoniae with acquired extended spectrum beta-lactamase genes
            isolated from chronic wounds in Ghana
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2348)
  AUTHORS   Pankok,F. and Taudien,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-APR-2022) Insitute of hospital hygiene and infection
            control, University Medical Center Goettingen (UMG), Humboldtallee
            34A, Goettingen, Lower Saxony 37073, Germany
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 13-FEB-2022
            Assembly Method                   :: Unicycler v. v0.4.8
            Assembly Name                     :: BNI_Ecoli_Iso00041_hybrid
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x
            Sequencing Technology             :: Oxford Nanopore PromethION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022964895.1-RS_2024_06_03
            Annotation Date                   :: 06/03/2024 03:48:46
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,036
            CDSs (total)                      :: 4,913
            Genes (coding)                    :: 4,651
            CDSs (with protein)               :: 4,651
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 262
            CDSs (without protein)            :: 262
            Pseudo Genes (ambiguous residues) :: 0 of 262
            Pseudo Genes (frameshifted)       :: 75 of 262
            Pseudo Genes (incomplete)         :: 193 of 262
            Pseudo Genes (internal stop)      :: 50 of 262
            Pseudo Genes (multiple problems)  :: 52 of 262
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP095158.1.
            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..2348
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="Iso00041"
                     /isolation_source="Chronic wound"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pIso00041_03"
                     /geo_loc_name="Ghana: Asante Akyem District"
                     /collection_date="2016"
     gene            366..1112
                     /locus_tag="MU410_RS25050"
     CDS             366..1112
                     /locus_tag="MU410_RS25050"
                     /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="helix-turn-helix domain-containing protein"
                     /protein_id="WP_071681991.1"
                     /translation="MDIGNILNESLNVEYSKLDLFLEKYDLTPEQKVEVYEFHAKASKK
                     NKTLVISETKENRFKSISEGVEYVHLFPKNLKILIKKYGLNTNELLVLTEIMESMLSHG
                     NLLINFSQKTLCELTEINKSTMSKTFKSLKQKQCLIEKNGHIYLNSVIFMKGLPHKLFI
                     QFRDHFLNSISYKLDDEEEFEKVFDDNFIKAYEKNLKEIKKKKQQIKEKKISKALDNFE
                     KEISEEWKEKFKDEEENFEFGFESEM"
                     /name="helix-turn-helix domain-containing protein"
     gene            1480..2208
                     /locus_tag="MU410_RS25055"
     CDS             1480..2208
                     /locus_tag="MU410_RS25055"
                     /inference="COORDINATES: protein motif:HMM:NF012798.4"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0015074 - DNA integration [Evidence IEA];
                     GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="site-specific integrase"
                     /protein_id="WP_097725005.1"
                     /translation="MGNSKRNIKKLNDNFREDILDYAFAHNLKCANALAILYATGCRPD
                     ELQTGVTVNYDSKKNEIEFRIIGSKLNRRMRRGIGVRKIKVKINNENARFFKNIVDKFI
                     ENPMSYDHKIKIESAKAFSGYITKISKKLWPRKTYHASAYSFRHAKATELKNSDYDKIE
                     IAQIMGHASVRSQQSYGRKSKKSKGGFDDIADVETNVKPRGGDRLLRFKIANKNKAAAK
                     IADTSTPSSPPPAPVRRFKM"
                     /name="site-specific integrase"
     Typing          2270..2348
                     /name="Col(IRGK)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.0"
                     /coverage="100.0"
                     /evalue="2.96e-26"
ORIGIN
        1 atctgttact tgaaaaccaa tgatcttaaa aaccatctca aaagttgaaa atttcacccc
       61 cttagtgttc ttaaaattct tagatgttct taggagttaa aaaactactc tataaccatt
      121 gattttactg actttttaaa aaaggcagtt gtcaaaaact tcaaccgtag ttgtcaaatt
      181 cgtcaactct agttgtcaaa ttcgtcaact gaggttgtca aatccgacaa ctctagccag
      241 tttccaagta gaaactacag tttcaaaact gaaacttttt ctaccttttg caactcaatc
      301 tattgactag ttctttataa atgttaaaac atatatatag aaataaataa aaagaggagg
      361 tttctatgga tattggaaat atattaaatg agagtttgaa tgttgaatat tcaaaattag
      421 atttgttttt agaaaaatat gatttaacac ctgagcaaaa agtagaagtt tatgaatttc
      481 acgcgaaagc gtccaagaaa aataagactt tggttatttc ggaaacaaaa gaaaatagat
      541 ttaaatctat ttccgaaggt gttgaatatg tgcatttgtt tccgaaaaac ttaaaaattt
      601 taattaaaaa atatggttta aacacaaatg aattattggt tttaacggaa ataatggaat
      661 caatgctttc acacggaaat ttattaatta atttttcgca aaaaacactt tgcgaattaa
      721 cagaaattaa taaatctact atgtcgaaaa catttaaaag ccttaaacaa aagcaatgtt
      781 taattgagaa aaacgggcat atttatttaa attctgtaat atttatgaaa ggtttacctc
      841 ataaattgtt tattcaattt agagatcatt ttttaaattc aatttcttat aaattagatg
      901 atgaagaaga gtttgaaaaa gtcttcgacg ataattttat taaagcatat gaaaaaaatc
      961 tcaaagaaat taaaaagaaa aaacaacaga taaaagaaaa gaaaatatca aaagcattag
     1021 ataattttga aaaagaaatt tctgaagaat ggaaagaaaa atttaaagac gaagaggaaa
     1081 atttcgaatt tggttttgaa tctgaaatgt aaaatcgccc tcgccgggca ggcgaatccc
     1141 ttactgaaat agaataaatt ctattccact aagggatttt ttttatccat tgattctcca
     1201 catttcaaat attgacagca ttttccaccc ggttataaca gtactataag tagttgtttc
     1261 aacccgtctt tttgggtgga acaacaaggc attttaggga tagagcgaag cgaaggccat
     1321 aaaattgcca cccccaaccg ggggtcgttg ttcgatttga gcgatagcga aaaattgaac
     1381 ataagggggg agggtttggg ttttacggta tttcaaattt gagcaaagcg aatttttgaa
     1441 atttccggtt cttttaattt gcaatgagga aaaatcaata tgggtaattc aaaaagaaat
     1501 ataaaaaaac taaatgataa ttttagagag gatattttag attatgcgtt cgcgcacaat
     1561 ctaaaatgtg ctaacgcact tgctatttta tatgcgacgg gttgccgtcc ggacgaactc
     1621 caaaccggag ttacggtaaa ctatgacagc aaaaaaaatg aaattgaatt tagaataatt
     1681 ggatcaaaac taaatagaag aatgagaaga ggcatagggg ttagaaaaat aaaagtaaaa
     1741 atcaataatg aaaatgccag attttttaaa aacattgttg ataaatttat tgaaaaccca
     1801 atgtcatatg atcacaaaat aaaaattgaa agtgccaaag cattttccgg gtacataaca
     1861 aaaatatcga aaaagctatg gcccaggaaa acctatcatg cttctgcata ttcttttaga
     1921 catgcaaaag caacggaatt gaaaaattcc gattatgata aaatcgaaat agctcagatt
     1981 atgggccatg cctcagttag atctcagcag agttacggaa gaaagagcaa aaaaagcaaa
     2041 ggtggatttg atgacatcgc agatgtcgaa accaatgtta aaccccgtgg cggtgataga
     2101 ttattgagat ttaagatcgc aaataaaaac aaagcagcgg caaaaattgc cgatacttcc
     2161 acccccagca gtcctccacc ggctcccgtt cgtcgcttca aaatgtgaac cgtgagcagt
     2221 tcaggaggtc ccctcctgga ctgtgaaggg ttggcccgtc cggcaggacg gttttatagc
     2281 aacatcctcc atagcgaagc agaagcccgg aacgggtaac ctggagggtt ttcccccgtg
     2341 ggggattg
//
