LOCUS       NZ_CP147041             3373 bp    DNA     circular CON 22-APR-2024
DEFINITION  Escherichia coli strain 21F61 plasmid p21F61_4, complete sequence.
ACCESSION   NZ_CP147041
VERSION     NZ_CP147041.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN39992807
            Assembly: GCF_038396565.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3373)
  AUTHORS   Gomi,R.
  TITLE     Genomic analysis of environmental Escherichia coli carrying
            transferable quinolone resistance determinants
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3373)
  AUTHORS   Gomi,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-MAR-2024) Department of environmental engineering,
            Kyoto University, KyotoDaigakuKatsura, Nishikyo-ku, Kyoto-city
            615-8540, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Flye v. 2.9.1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 150x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_038396565.1-RS_2024_04_20
            Annotation Date                   :: 04/20/2024 18:26:42
            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)                     :: 4,859
            CDSs (total)                      :: 4,740
            Genes (coding)                    :: 4,562
            CDSs (with protein)               :: 4,562
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 178
            CDSs (without protein)            :: 178
            Pseudo Genes (ambiguous residues) :: 0 of 178
            Pseudo Genes (frameshifted)       :: 73 of 178
            Pseudo Genes (incomplete)         :: 128 of 178
            Pseudo Genes (internal stop)      :: 31 of 178
            Pseudo Genes (multiple problems)  :: 48 of 178
            Pseudo Genes (short protein)      :: 4 of 178
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP147041.1.
            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..3373
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="21F61"
                     /isolation_source="river water"
                     /db_xref="taxon:562"
                     /plasmid="p21F61_4"
                     /geo_loc_name="Japan"
                     /collection_date="2021"
                     /collected_by="Fumie Adachi"
     gene            complement(join(3326..3373,1..186))
                     /locus_tag="WAZ52_RS24250"
                     /old_locus_tag="WAZ52_24250"
     CDS             complement(join(3326..3373,1..186))
                     /locus_tag="WAZ52_RS24250"
                     /old_locus_tag="WAZ52_24250"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137389.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137389.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHEVTQRNNA
                     ILNERVVILSQQVQRLAGQVDRLSRLFIANNS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(193..753)
                     /locus_tag="WAZ52_RS24255"
                     /old_locus_tag="WAZ52_24255"
     CDS             complement(193..753)
                     /locus_tag="WAZ52_RS24255"
                     /old_locus_tag="WAZ52_24255"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_000067487.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKKQLDTLSTTVSMQFSTTEAELSRQQKKLLWRVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            complement(<785..1441)
                     /locus_tag="WAZ52_RS24260"
                     /old_locus_tag="WAZ52_24260"
                     /pseudo=""
     CDS             complement(<785..1441)
                     /locus_tag="WAZ52_RS24260"
                     /old_locus_tag="WAZ52_24260"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(1431..1754)
                     /locus_tag="WAZ52_RS24265"
                     /old_locus_tag="WAZ52_24265"
     CDS             complement(1431..1754)
                     /locus_tag="WAZ52_RS24265"
                     /old_locus_tag="WAZ52_24265"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_024132211.1"
                     /translation="MLTIRVTDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1818..2009
                     /locus_tag="WAZ52_RS24270"
                     /old_locus_tag="WAZ52_24270"
     CDS             1818..2009
                     /locus_tag="WAZ52_RS24270"
                     /old_locus_tag="WAZ52_24270"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_000165979.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNDLDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(2091..2171)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.805"
                     /coverage="93.0"
                     /evalue="8.68e-18"
     Typing          complement(3..1441)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.042"
                     /coverage="91.0"
                     /evalue="0.0"
ORIGIN
        1 ggctaatctc tgcacctgct gactcaatat cacgacgcgc tcgttcagta tcgcgttgtt
       61 ccgttgcgta acctcgtgca tcttctgcaa ttccgcgaag gcgctctccc actcgttcag
      121 ccgccgcata tagtcctgtt gcaaatgctc taaggcgttc agcaaatgcc cttccagttc
      181 cgtcatactc gtttactccc tgaccagcct cacggcgttc ttgtcgccca ccgtccaggt
      241 gttttcccct ttcaccccgt ccggcaacac cagaaatttc ccgttctcgc cattgacgaa
      301 cgtcaccccc caggtttttg cctcgagttt cgccagcgtg ttttcctgct ctctgatagt
      361 caggatattt ttcgcaatct tgctttcctg ccactccatc agcccccagc accccaggaa
      421 aatgccgccc gtgacgctga gcgcggtcag cgccggaaac agtatccgcc ctttgatcac
      481 ccgccagagc agttttttct gctgccggga cagttcggcc tctgtggtgc tgaactgcat
      541 gctcacggtg gtgctcagcg tatccagttg ctttttcacg gatgttgtat gttcgctgat
      601 agcgtctctg attttctgcc tgtttaagct caatgccttg tctacagact cttcgagctt
      661 cctgaactcg ctgttcagca tgttctcggt agaagcggct cgctctttca gtttcttctc
      721 gaagtctgtt cccatttgta aaagattgct catacagcgc cccctttagc ctgagattcc
      781 gccccccctc cgggtcggca atactgatgc tgcttttggt tgtcctcacc acctcaaaac
      841 ctgccgctgt aagcgcctct gtgacatcct gacgcgtttt tattgctccg gcatggtaaa
      901 gagcctcaag accccgtgta atcgcttctg cggcctcctg tttcgctttt ggcagattat
      961 ttggcgtgac aagcgtccgt ctgttctccg gtgcgttcgg gtcacgcagc ccgtaatgat
     1021 gattaaccag cgtctgccag gcatttatcc tcggcctgtc cgcgcggtcg tagtacggct
     1081 ggaggcgctt accgctctgt agctccatgt tcgggatgac aaaattcagt tcgagccgcc
     1141 ccttatcctg gtgttccacc cagagaatgc tgtactggtc tttttcgaga ccgggcataa
     1201 gaacacgctc aaagctcgtc atcactcttt cgcgttcacc cggcggtaac tccttctccg
     1261 cgaacgacag aacgcctgaa gtgtatttct tcgagaatgg cgtggaatca atgagttccc
     1321 gcacttcttc cgggttaccc cggagcaccg ttgcgccttc gcggttacgc tcccgcccca
     1381 gcaggtaatc gaccgggcca cttccaccgc ctttccccct ggcatgaaat ttaactatca
     1441 tcccgtaccc cctgttccct gacagcctgc cgcaactggc gcaattcacc ctcgatggcc
     1501 atcagtgcgg ccaccacatg aacccggtca atcgaagacc actggccgct gttcaccttc
     1561 cgggctgtct ggttcaggtt gttcccgatg gcagccagat gccgcagcaa tggcggcgat
     1621 agtgtcggca gttttcctgt gcgtgcaacc ggctccccca gacagacccg ccgcatccat
     1681 tccgccagtc gtttaccctc gcagcgttcc agtaaccggg cgtgctcctc atcggtaacc
     1741 cgtatcgtga gcatcttctc gcgtttcatc ggtatcattc cccctaacaa atcccccata
     1801 caaggagcct taagaccatg accaaacagg aaaaaacagc ccttaacatg gctcgcttta
     1861 tcagaagcca gacgctaacc ctgctggaaa aactcaacga tctggacgcg gacgaacagg
     1921 cagacatctg cgaatcactt cacgaccacg ccgacgaact ctaccgcagt tgcctcgcac
     1981 gcttcggcga tgacggtgaa agcaactgaa acatgcagct cccggagacg ttcacagctt
     2041 gcctgtgagc ggatgccggg agcagacaag cccgccaggg cgcgtcagtg cgggtgtcgg
     2101 ggcgcagccc tgacccagtt cacagagcga tagcgatgtg tatactggct tatctcattt
     2161 tgcatcggtg cagaatggat gggaagtgca ccatgtcagg agtaaaaagc cgcacagatg
     2221 taaaaacagc gcacccgata aacagcacac acgcggacac tggcacaggc gcgtaagtgc
     2281 acaatgcttg catctgtgac tcttccgctt cctcgcccac tcgctcacta cgttcggtcg
     2341 ctggggctgc ggcgagcggt gggatcactc tcgttgtgat gctgatccgt tttttttttt
     2401 ttgcactgga gttatcagga gttgcggtgc acatgggatc gtgcgatatg ccggatggtg
     2461 aaaggttgga gggaacggca acaactcacc cctcccagtg aagggacggg tagtttgccg
     2521 ctctcgatat gccggacgga gccaaggcca tcgatcacgg ggcgcgtcag tggaagaacc
     2581 cgcgcctgcg tgacgtatgc gtcttcgccg caccatctca cccgtcacgc caccacatac
     2641 cgggaactgc cgccaaggtc taactcaacc aatctagccg cgctacatac ggtttttgtg
     2701 gcaactcatc aggtgtccgc tgtcgatgaa actctctgcg ccggtagcgg aactctcacg
     2761 cgtgcggtcg ccgtcgtcac agctccccca accgcaaacg attctcgcaa atacgcaagt
     2821 atctgcaaaa acaggttttt ttcggggttc ctgggagact gtgctgttga aaaattcttg
     2881 aagaatacag aaggctcatg caaactgaat gaactggttt ctgttgtgga tctcaacagt
     2941 ttccacagga acattgagga ggtcagagac ctcaatgaac ccgaaacagc tcgccttcct
     3001 ggcgagctgt tttcgttcta cgcccgccga cgaaagatcg caagtgcaat aacgagattt
     3061 ttcacgtctt tacgctcaaa aagtaaaaaa accatgtttt cccctggctg aatccccaaa
     3121 aacgcgtgaa atgcgttttc aggatgttgc atagctatgc acaaatacgg cacacgattt
     3181 gtttcgctcg ccccagccgt cgaactggtc aaaatggcaa gatttcgtca cttccccggt
     3241 cacatctcca ttgatggccc actccgaacc cgtgccgcgc gttcctgtac ctcatgtctg
     3301 taccgggcac gctcctgttc atcccttagc tgttgttcgc gataaataac cgactcaagc
     3361 gatccacttg ccc
//
