LOCUS       NZ_CP055051             4285 bp    DNA     circular CON 01-MAY-2024
DEFINITION  Escherichia coli strain SWHEFF_58 plasmid unnamed3, complete
            sequence.
ACCESSION   NZ_CP055051
VERSION     NZ_CP055051.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925585
            Assembly: GCF_022354045.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4285)
  AUTHORS   Che,Y., Xu,X., Yang,Y., Brinda,K., Hanage,W., Yang,C. and Zhang,T.
  TITLE     High-resolution genomic surveillance elucidates a multilayered
            hierarchical transfer of resistance between WWTP- and
            human/animal-associated bacteria
  JOURNAL   Microbiome 10 (1), 16 (2022)
   PUBMED   35078531
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 4285)
  AUTHORS   Che,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (10-JUN-2020) Civil Engineering, The University of Hong
            Kong, Pokfulam Road, Hong Kong 000000, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: "Other" v. Unicycler
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 200x
            Sequencing Technology :: Illumina; Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022354045.1-RS_2024_05_01
            Annotation Date                   :: 05/01/2024 05:27:04
            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)                     :: 4,944
            CDSs (total)                      :: 4,824
            Genes (coding)                    :: 4,684
            CDSs (with protein)               :: 4,684
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 140
            CDSs (without protein)            :: 140
            Pseudo Genes (ambiguous residues) :: 0 of 140
            Pseudo Genes (frameshifted)       :: 52 of 140
            Pseudo Genes (incomplete)         :: 90 of 140
            Pseudo Genes (internal stop)      :: 30 of 140
            Pseudo Genes (multiple problems)  :: 29 of 140
            Pseudo Genes (short protein)      :: 3 of 140
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP055051.1.
            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..4285
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SWHEFF_58"
                     /isolation_source="Shek Wu Hui WWTPs_58 WWTPs effluent"
                     /db_xref="taxon:562"
                     /plasmid="unnamed3"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.5 N 114.1 E"
                     /collection_date="2018-12"
     gene            complement(join(4008..4285,1..733))
                     /locus_tag="HUZ70_RS24640"
                     /old_locus_tag="HUZ70_24465"
     CDS             complement(join(4008..4285,1..733))
                     /locus_tag="HUZ70_RS24640"
                     /old_locus_tag="HUZ70_24465"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000395670.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001522447.1"
                     /translation="MEFQELENSACLYWPKELAERAASISAISPLIETQDEFLSILTIS
                     TNKPTSCFDAVRLCNKISPNLFVKHLMVLSDIGGERLHRFFKDLDKIYPDRIMEFNIGN
                     NSYSYQFNSNRAWTTKNLNVEKSRLLQPVSDFTREMLDVCMLILWGGNTINNTNLPTEI
                     ENNCILGNLIGNKEAIEQFVKERYIMVSRQTGGATANDLGHICEIFIKEKLYKLIDDNI
                     SLDGHHIDGVTHNDKDLTTFDIVAKNTITKKCVGIEISFQVTTNSTIERKAGLAKSRRD
                     LLNSIGHKIAYVIDGSGNFQRSNAIKTIINHSDMTVNFSDNGINSLATFICETLK"
                     /name="hypothetical protein"
     gene            complement(961..1092)
                     /locus_tag="HUZ70_RS24790"
     CDS             complement(961..1092)
                     /locus_tag="HUZ70_RS24790"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001318243.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_071791513.1"
                     /translation="MHEPPVQPDRCALSGNCRLESNPERHAKAPLAAAIGRGCTRNC"
                     /name="replication initiation protein"
     gene            complement(1756..1950)
                     /locus_tag="HUZ70_RS24645"
                     /old_locus_tag="HUZ70_24470"
     CDS             complement(1756..1950)
                     /locus_tag="HUZ70_RS24645"
                     /old_locus_tag="HUZ70_24470"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_001041631.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQIRFEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(2764..4011)
                     /locus_tag="HUZ70_RS24650"
                     /old_locus_tag="HUZ70_24475"
     CDS             complement(2764..4011)
                     /locus_tag="HUZ70_RS24650"
                     /old_locus_tag="HUZ70_24475"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001522448.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA cytosine methyltransferase"
                     /protein_id="WP_001522448.1"
                     /translation="MIKFVDLFSGTGGIRLGFEQAMKEIGLSTKCVKSSEIDKKACETY
                     KLNFDEESYCDIHDVDIDESFDVLLAGFPCQAFSYAGKQLGFADTRGTLFFEVERIIKK
                     NKPKLCLLENVRGLTSHDKGRTFSTILKSLHDLGYHVEYRLLNTSNFGVPQNRVRIYII
                     ASLKKEVTLTIPNDLGAKDTHNYKPSKGGHDFYTESKVSDILEDSPDKSYDCSDWFKQR
                     LEDIFKGDLNKVHGIRLIDTRNGNSLHSWDLGLKGECSNDEIAFMNSLIANRRKHIFGT
                     HQDGKALSKAQIETFFKHSETTNIIKNLIKKGYLKEKNGLYNPVCGNMSFEVFKFLDPN
                     KVSITLTASDANRLGVYHNNRLRRLTPRECARLQGYPDSYILHPKDSMAYKQLGNAVSV
                     PVIKNIFLDIMKNNFI"
                     /name="DNA cytosine methyltransferase"
     Typing          1591..1676
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="8.58e-38"
     Typing          1987..2085
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          2210..2464
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.512"
                     /coverage="89.0"
                     /evalue="1.21e-116"
     Typing          complement(1021..1569)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.414"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 caatatcaaa agtcgtaagg tctttatcgt tatgagttac accatcgata tggtgtccat
       61 ctagagatat attatcatca ataagtttat aaagtttttc ttttataaag atctcgcata
      121 tgtgtccaag atcatttgcc gttgcacctc ctgtttgtct gctaaccatt atatatcttt
      181 cttttacaaa ttgttctatt gcttctttgt tcccaattaa atttcccaaa atacagttat
      241 tttctatttc agttggaagg tttgtattgt ttatagtgtt acctccccaa aggatcagca
      301 tgcaaacatc aagcatttct cgtgtaaaat cacttacagg ttgcaaaagt cgtgattttt
      361 ccacgtttaa attcttggtt gtccatgctc tattgctatt gaattggtaa gagtaagagt
      421 tattccctat attgaactcc attattctgt caggatagat tttatctaaa tctttaaaaa
      481 agcgatgaag tctttcgcct ccaatatctg acaaaaccat taggtgcttg acaaataggt
      541 tgggtgatat cttattgcat aaccgtacag catcaaaaca agatgtaggc ttatttgttg
      601 atattgttag tattgataaa aattcatctt gggtctctat aagagggctt atggcgctaa
      661 tagatgctgc tctttctgca agttctttgg gccagtataa gcatgcgcta ttttctaatt
      721 cttggaactc catgattatt ccttggtaaa actatccaaa tagaccttga gttacacccc
      781 tatgatgggt aatctctacg ggcgtaaacg aaaaaaccca cgttctcagg cgtgggtttt
      841 tcgaaggtta gaagtttctc aggctttcta acccaaggta acagggcgta caagaccgct
      901 gccaccaaat ctgtcctttc agtgtagccg cagtcgggcc ttcacttcaa gaactccgta
      961 tcagcaattt cttgtacacc ctctaccaat ggctgctgcc agtggtgctt ttgcatgtct
     1021 ttccgggttg gactcaagac gacagttacc ggataaggcg cagcggtcgg gctgaacggg
     1081 gggttcgtgc acacagccca gcttggagcg aacgacctac accgaactga gataccaaca
     1141 gcgtgagcta tgagaaagcg ccacgcttcc cgaagggaga aaggcggaca ggtatccggt
     1201 aagcggcagg gtcggaacag gagagcgcac gagggagctt ccagggggaa acgcctggta
     1261 tctttatagt cctgtcgggt ttcgccacct ctgacttgag cgtcggtttt tgtgatgctc
     1321 gtcagggggg cggagcctat ggaaaaacgc cagcggcgtg gccttttccg ggttctcgtt
     1381 ttttgctcac atgtttcttt tggcgttatc ccctgattct gtggataacc gcatctccgc
     1441 ttttgagtga gccgacaccg ctcgccgcag ccgaacgacc gagcgtagcg agtcagtgag
     1501 cgaggaagcg gaagagcgcc ggaacgtgca ttttctcctt acgcatctgt gcggcatttc
     1561 acaccgcata tggcgctctt ttcttacaat ctgcactgat gccgcatggt taagccagta
     1621 tacactccgc tatcgctacg tgactgggtc atggctgcgc cccgacaccc gctaaaaccc
     1681 cctgacgcgc cctgacgggc ttgtctgctg acgaaaacgc ccacgggaaa gccgtgaccg
     1741 cctccgtcag cttcgttatg ttcctgtttc actttcggcc tcaaagcgaa tctggatgct
     1801 gttctggagt tcttctgcga gttcgtgcag tcgttcgcac atggccgcct gttcgtcggc
     1861 atccagagca tccagttttt caagcagtgt caggctctgg cttttgataa atcgcgccat
     1921 attcagcgca gtttgttgtt gtttgttcac cttccgttgt tctccgtcag ttccgggtgt
     1981 cggggggacc ctgagcaggt ggtaattgta agacgttgcg ggcgacggta ttacaattgc
     2041 acatcctgtc ctgtttcttt aggacgtatc atggcacagc atatcaactg ataaataatc
     2101 cctgtgcagt gcagccgctg ttgcataaaa tttcgctctg cgtcgagtgt ttcttaatca
     2161 ataattccgc tgatactccg gaaaaacgcg agtctgttct catgcctgaa atgcccacac
     2221 cccacgcaaa aacaagtttt tgctgatttt tctttataaa tagagagtta tgacaaatta
     2281 gttcttcttg ctctctttgt gatatttaaa aaagcggtgt cggcgcggtg ttgtagctgc
     2341 gcaacaccgc tttttagggg tggtactgac tattttcata aaaaacatca tcttatatta
     2401 ggggtgctgc tagcggcgcg gtgtgttttt ttacaggaca cccctggggg cgctgctagg
     2461 ggtgtctgtt cagatatgta gcaatgagtc agggattcac gaactgaaaa tgtccgaaaa
     2521 tgtgtctcat gggcactgta tgcgcccaaa ccgatcgtca ttcactttca tgcatagcta
     2581 tgcagtgagc tgaaagcgat cctgacgcat ttttccggtt taccccgggg agaacatctc
     2641 tttttgcggt gttcgcggca gaatcgcgtt cagcgcgttt tagcggtgcg cgcaatgcga
     2701 cattatggta aatctgttaa atttaattaa ataaccatag agcagttttg ctagtaatat
     2761 agtttatatg aagttattct tcattatatc aagaaaaata tttttaatga ctggaacgct
     2821 tacagcattc cccaattgtt tatatgccat gctatctttt gggtgtaaga tatatgagtc
     2881 tgggtaacct tgtagccttg cacattctct tggtgtaagg cgtcgcagtc tattgttgtg
     2941 atagactcca agtctattgg catcagatgc agtaagtgta attgacactt tatttgggtc
     3001 aaggaatttg aatacttcaa aagacatatt tccgcaaact gggttgtata gtccgttttt
     3061 ttctttaagg taaccctttt taattagatt ttttattatg ttggtggttt cgctatgttt
     3121 gaaaaatgtt tcaatttgtg cttttgacaa agccttgccg tcttggtgtg tgccaaaaat
     3181 atgctttcta cgatttgcaa ttaatgaatt catgaaagct atttcatcat ttgagcactc
     3241 gccttttagc ccaagatccc aagagtgcaa ggagttgccg ttccttgtgt caattagcct
     3301 gattccatga actttattca ggtcaccttt aaaaatatct tcaaggcgtt gcttgaacca
     3361 atcgctgcaa tcatatgact tgtctggact atcctctagt atgtcagaaa cttttgattc
     3421 tgtataaaaa tcatgaccac ctttggatgg tttgtaattg tgcgtatctt tggctccaag
     3481 atcattagga atagtaagcg ttacctcttt ttttaatgag gctattatat atattctaac
     3541 cctattttga gggacgccaa aattacttgt atttaatagt ctgtattcaa catgataccc
     3601 taaatcgtga agggatttta atattgttga aaatgtcctt cctttatcat gtgaagttaa
     3661 tccacgtaca ttctccaaaa gacacaattt aggcttgttt ttctttataa ttctttctac
     3721 ttcaaaaaat aatgtacctc gggtgtctgc aaaaccaagt tgttttccag cataagagaa
     3781 tgcttggcaa ggaaatcctg ccaataaaac atcgaagctt tcatctatat caacatcatg
     3841 tatatcacaa tatgattctt cgtcgaagtt aagtttgtat gtttcgcatg cttttttgtc
     3901 aatttctgag ctttttacac attttgttga caatccaatt tctttcatgg cttgctcaaa
     3961 accaagtcta ataccacctg tgccagaaaa aaggtcaaca aatttaatca tttcaatgtc
     4021 tcgcagatga atgttgctag tgaatttata ccattatctg aaaagttaac agtcatgtca
     4081 ctatggttaa ttattgtttt tatggcattt gagcgctgaa aattaccaga cccatcaatc
     4141 acatatgcta ttttatgccc tattgaattg agtaaatctc ttctgctttt ggctaatcct
     4201 gcttttcttt ctattgttga gtttgttgta acttgaaaac ttatttcaat accaacacat
     4261 ttttttgtta tcgtgttttt tgcta
//
