LOCUS       NZ_CP092977             6200 bp    DNA     circular CON 24-MAY-2024
DEFINITION  Escherichia coli strain WCHEC005215 plasmid p1_005215, complete
            sequence.
ACCESSION   NZ_CP092977
VERSION     NZ_CP092977.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN06209720
            Assembly: GCF_022559685.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6200)
  AUTHORS   Long,H., Feng,Y. and Zong,Z.
  TITLE     The complete genome of Escherichia coli strain 005215
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6200)
  AUTHORS   Long,H., Feng,Y. and Zong,Z.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-MAR-2022) Center of Infectious Diseases, West China
            Hospital, Sichuan University, Guoxuexiang 37, Chengdu, Sichuan
            610041, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: Trycycler v. 0.5.3; Flye v. 2.9; Raven v. 1.8.0;
            Miniasm v. 0.3
            Genome Representation             :: Full
            Expected Final Version            :: No
            Genome Coverage                   :: 150.0x
            Sequencing Technology :: Illumina HiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022559685.1-RS_2024_05_24
            Annotation Date                   :: 05/24/2024 04:43:40
            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)                     :: 5,008
            CDSs (total)                      :: 4,888
            Genes (coding)                    :: 4,629
            CDSs (with protein)               :: 4,629
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 259
            CDSs (without protein)            :: 259
            Pseudo Genes (ambiguous residues) :: 0 of 259
            Pseudo Genes (frameshifted)       :: 85 of 259
            Pseudo Genes (incomplete)         :: 175 of 259
            Pseudo Genes (internal stop)      :: 57 of 259
            Pseudo Genes (multiple problems)  :: 52 of 259
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP092977.1.
            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..6200
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="WCHEC005215"
                     /isolation_source="Rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p1_005215"
                     /geo_loc_name="China: Sichuan, Chengdu"
                     /collection_date="2013-09"
     gene            1..159
                     /locus_tag="MM176_RS24795"
                     /old_locus_tag="MM176_24830"
     CDS             1..159
                     /locus_tag="MM176_RS24795"
                     /old_locus_tag="MM176_24830"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354639.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032287700.1"
                     /translation="MHEPPVQSDRCALSGNYQLESNPERHDKTPLAAAISNRSAREDRL
                     RGLEVEA"
                     /name="hypothetical protein"
     gene            619..1434
                     /gene="sul2"
                     /locus_tag="MM176_RS24800"
                     /old_locus_tag="MM176_24835"
     ARG             620..1431
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            1495..2298
                     /gene="aph(3'')-Ib"
                     /locus_tag="MM176_RS24805"
                     /old_locus_tag="MM176_24840"
     ARG             1496..2295
                     /name="aph(3'')-Ib"
                     /gene="aph(3'')-Ib"
                     /gene_name="aminoglycoside O-phosphotransferase
                     APH(3'')-Ib"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            2298..3134
                     /locus_tag="MM176_RS24810"
                     /old_locus_tag="MM176_24845"
     CDS             2298..3134
                     /locus_tag="MM176_RS24810"
                     /old_locus_tag="MM176_24845"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000480972.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="APH(6)-I family aminoglycoside
                     O-phosphotransferase"
                     /protein_id="WP_094885524.1"
                     /translation="MFMPPVFPAHWHVSQPVLIADTFSSLVWKVSLPDGTPAIVKGLKP
                     IEDIADELRGADYLVWRNGRGAVRLLGRENNLMLLEYSGERMLSHIVAEHGDYQATEIA
                     AELMAKLYAASEEPLPSALLPIRDRFAALFQRARDDQNAGCQTDYVHAAIIADQMMSNA
                     SELRGLHGDLHHENIMFSSRGWLVIDPVGLVGEVGFGAANMFYDPADRDDLCLDPRRIA
                     QMADAFSRALDVDPRRLLDQAYAYGCLSAAWNADGEEEQRDLAIAAAIKQVRQTSY"
                     /name="APH(6)-I family aminoglycoside O-phosphotransferase"
     gene            complement(<3241..3645)
                     /locus_tag="MM176_RS24815"
                     /old_locus_tag="MM176_24850"
                     /pseudo=""
     CDS             complement(<3241..3645)
                     /locus_tag="MM176_RS24815"
                     /old_locus_tag="MM176_24850"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001120888.1"
                     /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="IS91 family transposase"
                     /name="IS91 family transposase"
     gene            complement(3689..4078)
                     /locus_tag="MM176_RS24820"
                     /old_locus_tag="MM176_24855"
     CDS             complement(3689..4078)
                     /locus_tag="MM176_RS24820"
                     /old_locus_tag="MM176_24855"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000102614.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000102614.1"
                     /translation="MSTELNSGTVGGFGHMGPNDPYNDGHSGSGSSGGSFNGGGNGGHD
                     NSSGSSYTASFGLITGRHPITVPGTKNINSVDLSAVINNIIHHEGARNNMYLDTANNVR
                     VGVTGTGWQCLATAGISAEGKRTFR"
                     /name="hypothetical protein"
     gene            4296..4736
                     /locus_tag="MM176_RS24825"
                     /old_locus_tag="MM176_24860"
     CDS             4296..4736
                     /locus_tag="MM176_RS24825"
                     /old_locus_tag="MM176_24860"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011161230.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_005119689.1"
                     /translation="MAWHTVQETLKLTGKSRSQLYRDMAKGLVSYRTGKNDRREFETSE
                     LIRAYGELRTSETPKRHKEGHSKSVVSQAENAQLDVIQQKLDALQQTVTLMLEDKMARE
                     AENRLRNEEREQLQAEISRLADALAQEKKRGFWSRLFRSGSE"
                     /name="hypothetical protein"
     gene            complement(5481..5630)
                     /locus_tag="MM176_RS24830"
                     /old_locus_tag="MM176_24865"
     CDS             complement(5481..5630)
                     /locus_tag="MM176_RS24830"
                     /old_locus_tag="MM176_24865"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001138880.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGSPVG
                     REAL"
                     /name="hypothetical protein"
     ARG             2299..3131
                     /name="aph(6)-Id"
                     /gene="aph(6)-Id"
                     /gene_name="aminoglycoside O-phosphotransferase APH(6)-Id"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="99.64"
                     /coverage="100.0"
     Typing          complement(5666..5839)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          2..119
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.215"
                     /coverage="94.0"
                     /evalue="7.36e-44"
     Typing          5763..6200
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.403"
                     /coverage="99.0"
                     /evalue="1.5000000000000002e-168"
ORIGIN
        1 atgcacgaac cccccgttca gtccgaccgc tgcgccttgt ccggtaacta tcaacttgag
       61 tccaacccgg aaagacacga caaaacgcca ctggcagcag ccattagtaa caggagtgca
      121 cgagaagata gattaagagg tcttgaagta gaggcctgac tgcggctaca ctgaaagaac
      181 agttttggta atggcggtct cgtgaaccct gttaccgggt taagcagttc cccaactgac
      241 ttaaccttcg aacaaaccgc ctccccaggc ggttttttcg tttacagagc aagagattac
      301 gattcattga aaaggatctc aagaagatcc tttgtagatt actatcaatt aatcttccga
      361 acatgacacc agtcactgtt gattacggtt aaaccgctcc gtaacaggtt tccctcgtat
      421 tggtgacttg cagcaccaaa gaagcaaaaa agataaatat atctacttat tgagagatga
      481 tatatttatt tccaaaatgc tacagataca tcatcatgaa acggatcacc gcaaacaggt
      541 tactcgcctg gggattccct ttcgacccga gcatccgtat gagactcatg ctcgattatt
      601 attattatag aagcccccat gaataaatcg ctcatcattt tcggcatcgt caacataacc
      661 tcggacagtt tctccgatgg aggccggtat ctggcgccag acgcagccat tgcgcaggcg
      721 cgtaagctga tggccgaggg ggcagatgtg atcgacctcg gtccggcatc cagcaatccc
      781 gacgccgcgc ctgtttcgtc cgacacagaa atcgcgcgta tcgcgccggt gctggacgcg
      841 ctcaaggcag atggcattcc cgtctcgctc gacagttatc aacccgcgac gcaagcctat
      901 gccttgtcgc gtggtgtggc ctatctcaat gatattcgcg gttttccaga cgctgcgttc
      961 tatccgcaat tggcgaaatc atctgccaaa ctcgtcgtta tgcattcggt gcaagacggg
     1021 caggcagatc ggcgcgaggc acccgctggc gacatcatgg atcacattgc ggcgttcttt
     1081 gacgcgcgca tcgcggcgct gacgggtgcc ggtatcaaac gcaaccgcct tgtccttgat
     1141 cccggcatgg ggttttttct gggggctgct cccgaaacct cgctctcggt gctggcgcgg
     1201 ttcgatgaat tgcggctgcg cttcgatttg ccggtgcttc tgtctgtttc gcgcaaatcc
     1261 tttctgcgcg cgctcacagg ccgtggtccg ggggatgtcg gggccgcgac actcgctgca
     1321 gagcttgccg ccgccgcagg tggagctgac ttcatccgca cacacgagcc gcgccccttg
     1381 cgcgacgggc tggcggtatt ggcggcgctg aaagaaaccg caagaattcg ttaactgcac
     1441 attcgggata tttctctata ttcgcgcttc atcagaaaac tgaaggaacc tccattgaat
     1501 cgaactaata ttttttttgg tgaatcgcat tctgactggt tgcctgtcag aggcggagaa
     1561 tctggtgatt ttgtttttcg acgtggtgac gggcatgcct tcgcgaaaat cgcacctgct
     1621 tcccgccgcg gtgagctcgc tggagagcgt gaccgcctca tttggctcaa aggtcgaggt
     1681 gtggcttgcc ccgaggtcat caactggcag gaggaacagg agggtgcatg cttggtgata
     1741 acggcaattc cgggagtacc ggcggctgat ctgtctggag cggatttgct caaagcgtgg
     1801 ccgtcaatgg ggcagcaact tggcgctgtt cacagcctat cggttgatca atgtccgttt
     1861 gagcgcaggc tgtcgcgaat gttcggacgc gccgttgatg tggtgtcccg caatgccgtc
     1921 aatcccgact tcttaccgga cgaggacaag agtacgccgc agctcgatct tttggctcgt
     1981 gtcgaacgag agctaccggt gcggctcgac caagagcgca ccgatatggt tgtttgccat
     2041 ggtgatccct gcatgccgaa cttcatggtg gaccctaaaa ctcttcaatg cacgggtctg
     2101 atcgaccttg ggcggctcgg aacagcagat cgctatgccg atttggcact catgattgct
     2161 aacgccgaag agaactgggc agcgccagat gaagcagagc gcgccttcgc tgtcctattc
     2221 aatgtattgg ggatcgaagc ccccgaccgc gaacgccttg ccttctatct gcgattggac
     2281 cctctgactt ggggttgatg ttcatgccgc ctgtttttcc tgctcattgg cacgtttcgc
     2341 aacctgttct cattgcggac accttttcca gcctcgtttg gaaagtttca ttgccagacg
     2401 ggactcctgc aatcgtcaag ggattgaaac ctatagaaga cattgctgat gaactgcgcg
     2461 gggccgacta tctggtatgg cgcaatggga ggggagcagt ccggttgctc ggtcgtgaga
     2521 acaatctgat gttgctcgaa tattccgggg agcgaatgct ctctcacatc gttgccgagc
     2581 acggcgacta ccaggcgacc gaaattgcag cggaactaat ggcgaagctg tatgccgcat
     2641 ctgaggaacc cctgccttct gcccttctcc cgatccggga tcgctttgca gctttgtttc
     2701 agcgggcgcg cgatgatcaa aacgcaggtt gtcaaactga ctacgtccac gcggcgatta
     2761 tagccgatca aatgatgagc aatgcctcgg aactgcgtgg gctacatggc gatctgcatc
     2821 atgaaaacat catgttctcc agtcgcggct ggctggtgat agatcccgtc ggtctggtcg
     2881 gtgaagtggg ctttggcgcc gccaatatgt tctacgatcc ggctgacaga gacgaccttt
     2941 gtctcgatcc tagacgcatt gcacagatgg cggacgcatt ctctcgtgcg ctggacgtcg
     3001 atccgcgtcg cctgctcgac caggcgtacg cttatgggtg cctttccgca gcttggaacg
     3061 cggatggaga agaggagcaa cgcgatctag ctatcgcggc cgcgatcaag caggtgcgac
     3121 agacgtcata ctagatatca agcgacttct cctatcccct gggaacacat caatctcacc
     3181 ggagaatatc gctggccaaa gccttagcgt aggattccgc cccttcccgc aaacgacccc
     3241 aaacaggaaa cgcagctgaa acgggaagct caacacccac tgacgcatgg gttgttcagg
     3301 cagtacttca tcaaccagca aggcggcact ttcggccatc cgccgcgccc cacagctcgg
     3361 gcagaaaccg cgacgcttac agctgaaagc gaccaggtgc tcggcgtggc aagactcgca
     3421 gcgaacccgt agaaagccat gctccagccg cccgcattgg agaaattctt caaattcccg
     3481 ttgcacatag cccggcaatt cctttccctg ctctgccata agcgcagcga atgccgggta
     3541 atactcgtca acgatctgat agagaagggt ttgctcgggt cggtggctct ggtaacgacc
     3601 agtatcccga tcccggctgg ccgtcctggc cgccacatga ggcatgttcc gcgtccttgc
     3661 aatactgtgt ttacatacag tctatcgctt agcggaaagt tcttttaccc tcagccgaaa
     3721 tgcctgccgt tgctagacat tgccagccag tgcccgtcac tcccactctt acattgttcg
     3781 cagtatctag gtacatgtta ttgcgtgcac cttcatgatg tataatgtta ttaatgacag
     3841 cagaaagatc gacagaatta atattcttcg tacctgggac agttatcggg tgtcggccag
     3901 tgatgagacc aaaggatgca gtataagatg aaccactact attatcatgg ccaccattac
     3961 caccaccgtt aaaactacct cccgaacttc cagagccgct atgaccatca ttgtaggggt
     4021 catttggtcc catgtgacca aaaccaccga cagtaccgct atttaactct gtactcataa
     4081 aattatcctc tttgactttt aaaaacagca aaaactgtat ttataacaat gtgtttatat
     4141 acagtattcg aaatactacg cccgtcaaaa ccacaccgtc aacaggtttt ttgtgtattt
     4201 ttcacgcctc acgggcagcc tcagaccttt tgtgttaaaa cagtaatatg ttctgctgtt
     4261 acaatacggt acacacagga gacactgtca cttttatggc atggcacaca gttcaagaga
     4321 cactgaaatt aacaggaaag tcgcgctcgc aattatatcg tgacatggct aaaggccttg
     4381 tcagctatcg cacaggaaaa aatgatcgcc gggagttcga gaccagtgaa ctgattcggg
     4441 cctatggcga gctgcgcact tctgagacac caaaaaggca caaggaggga cactccaaat
     4501 ctgtcgttag ccaggcggaa aatgctcagc tagacgtcat tcagcagaaa ctggacgctc
     4561 tgcagcagac tgttacccta atgcttgaag acaagatggc gcgggaagca gaaaaccgcc
     4621 tgcgaaatga ggagagggaa caactacagg ccgaaattag ccgtctggct gacgcgctgg
     4681 cacaggaaaa aaagcgggga ttctggtcgc ggctgtttcg ctccggttca gagtaacagt
     4741 gcaggtgact ctgatttacc ataacatctg ttatcagcac cgcctgagag gccctcaggg
     4801 cgtttctgac gggaaaccgg taaaacaggc aacaaaccac ccgaaaaccc gccagaaacg
     4861 cgcaggctct gtttttacgg catgcatgag tatgcgcaca agtgcatagc gcggaaattc
     4921 acaccattca gccggggtaa gtcctgtttc cggcgttctt cccatccgaa aacggtgaac
     4981 ggggacgcaa tttattgcgt ggccgtgaag cgttgccggc gcagccggaa aacccgctgt
     5041 cagcacgttc aggaaggggg tgatgtacaa atggcacaga ggatgaaagt gacgtatgag
     5101 ctgaaggaat gatgtaaaag tgatgtataa gtgatgtaaa agtgatgtat gaactgaagg
     5161 agcgatgtaa ttctgtagtc aggaagaata acccgttcat gcaggcatga acgatacagt
     5221 gaggaacgct ttttttgtca cgatctcccc ttaacctgcg taaatcaccc gccatggttg
     5281 attatttttc aacctcaaaa tggtcataca cctaacgcag ccgcgatttt catcgcaact
     5341 gcatgaatta aaagaaaaaa aaggaatatt tcgttttcac gagtaatacc cgggtattaa
     5401 aaatccactg taattacatg aaaataaaga aataaaaggt aataccggag tattaccacg
     5461 tacgcgggca agcgaaaaag ctataacgct tcccggccga caggcgaccc aaaatccaca
     5521 ggggcatgca ggttctcttc agtaacctgc gccattaaat caaaaaggtc atattcgccg
     5581 ggaagctgcg tatcagtcga atccagttgt tcatcatatt cagatggcat ggggtgatat
     5641 ccagtagctg agaggttgtt agcgggtttc ggggcgcagc cctgaaccag tcatgtagcg
     5701 ctagcggagt gtatactggc ttactatgtt gccacgattg cgaaaatcag tgaagtgctt
     5761 catgtggcag gagaaaaaag gcagcaccgg cgcgtcagca gaatatgcga tacaggagat
     5821 attccgcttc ctcgctcact gactcgctac gctcggtcgt tcggctgcgg cgagcggtac
     5881 cggcttacgg acggggacgg aaatttcctg gaagatacca ggaagacact tagcaaagaa
     5941 gagataaggc cacggcgaag ccgtttttcc ataggctccg cccccctgac aagcatcgca
     6001 aaatctgacg ctcaaatcag tggtggcgaa acccgacagg actataaaga tcccaggcgt
     6061 ttccccctgg tagctccctc gtgcgctctc ctgttcctgc ctttcggttt accggtgtca
     6121 ttccgctgtt atggccgcgg tttctcattc cacgcctgac actcagttcc gtgaaggcag
     6181 ttcgctccaa gctggactgt
//
