LOCUS       NZ_CP080061             4607 bp    DNA     circular CON 14-JUN-2024
DEFINITION  Escherichia coli strain 18SZHZ655Rt plasmid p655Rt_tetX4, complete
            sequence.
ACCESSION   NZ_CP080061
VERSION     NZ_CP080061.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN20339660
            Assembly: GCF_023516035.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4607)
  AUTHORS   Liu,B., Liu,W. and Fu,Y.
  TITLE     Genetic environment and risk factors analysis of mobile tigecycline
            resistance genes tet(X) variants in healthy human carriages: a
            cross-sectional and case-control study
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4607)
  AUTHORS   Liu,B., Liu,W. and Fu,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-JUL-2021) Key Laboratory of Genetics & Molecular
            Medicine of Shenzhen, Shenzhen Center for Disease Control and
            Prevention, Longyuan Road 8, Shenzhen 518055, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_023516035.1-RS_2024_06_14
            Annotation Date                   :: 06/14/2024 05:58:29
            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)                     :: 4,979
            CDSs (total)                      :: 4,858
            Genes (coding)                    :: 4,716
            CDSs (with protein)               :: 4,716
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 142
            CDSs (without protein)            :: 142
            Pseudo Genes (ambiguous residues) :: 0 of 142
            Pseudo Genes (frameshifted)       :: 66 of 142
            Pseudo Genes (incomplete)         :: 91 of 142
            Pseudo Genes (internal stop)      :: 26 of 142
            Pseudo Genes (multiple problems)  :: 35 of 142
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP080061.1.
            Bacteria and source DNA available from Shenzhen Center for Disease
            Control and Prevention.
            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..4607
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="18SZHZ655Rt"
                     /isolation_source="Human feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p655Rt_tetX4"
                     /geo_loc_name="China:Shenzhen"
                     /altitude="120 m"
                     /collection_date="2018-12-08"
                     /collected_by="Bang Liu"
     gene            complement(join(4299..4607,1..537))
                     /gene="estT"
                     /locus_tag="KZO13_RS24725"
                     /old_locus_tag="KZO13_24695"
     CDS             complement(join(4299..4607,1..537))
                     /gene="estT"
                     /locus_tag="KZO13_RS24725"
                     /old_locus_tag="KZO13_24695"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014053561.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="macrolide hydrolase EstT"
                     /protein_id="WP_164538741.1"
                     /translation="MKEKIIKTNGIELCTESFGNKKNPAILLVAGATVSMLYWDTEFCQ
                     QLSEKGFFVIRYDNRDVGKSTNYEPGSAPYDIVDLTNDAIAILDGYEIDKAHFVGMSLG
                     GLITQIAAIKFADRVSSLTLMSTGPWGDSDPTIPEMDTRILDFHGKAGTVDWSNEDSVV
                     NYLIQGAELMCGKKQFDKQRSEKLIRAEFNRANNYISMFNHATLQGSEEYWNRLNEVNQ
                     PTLIIHGTDDKIWHYKNAGVLIEKIQNTKLITLEGTGHELHFEDWTTIIDGIEKHINEQ
                     "
                     /name="estT"
     gene            complement(1320..2813)
                     /locus_tag="KZO13_RS24730"
                     /old_locus_tag="KZO13_24700"
     CDS             complement(1320..2813)
                     /locus_tag="KZO13_RS24730"
                     /old_locus_tag="KZO13_24700"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001120888.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS91-like element ISVsa3 family transposase"
                     /protein_id="WP_001120888.1"
                     /translation="MPHVAARTASRDRDTGRYQSHRPEQTLLYQIVDEYYPAFAALMAE
                     QGKELPGYVQREFEEFLQCGRLEHGFLRVRCESCHAEHLVAFSCKRRGFCPSCGARRMA
                     ESAALLVDEVLPEQPMRQWVLSFPFQLRFLFASRPEIMGWVLGIVYRVIATHLVKKAGH
                     THQVAKTGAVTLIQRFGSALNLNVHFHMLFLDGVYVEQSHGSARFRWVKAPTSPELTQL
                     THTIAHRVGRYLERQGLLERDVENSYLASDAVDDDPMTPLLGHSITYRIAVGSQAGRKV
                     FTLQTLPTSGDPFGDGIGKVAGSSLHAGVAARADERKKLERLCRYISRPAVSEKRLSLT
                     RGGNVRYQLKTPYRDGTTHVIFEPLDFIARLAALVPKPRVNLTRFHGVFAPNSRHRALV
                     TPAKRGRGNKVRVADEPATPAQRRASMTWAQRLKRVFNIDIETCSGCGGAMKVIACIED
                     PIVIKQILDHLKHKAETSGTRALPESRAPPAELLLGLFD"
                     /name="IS91-like element ISVsa3 family transposase"
     gene            complement(3152..4309)
                     /locus_tag="KZO13_RS24735"
                     /old_locus_tag="KZO13_24705"
     CDS             complement(3152..4309)
                     /locus_tag="KZO13_RS24735"
                     /old_locus_tag="KZO13_24705"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014615010.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="tetracycline-inactivating monooxygenase Tet(X4)"
                     /protein_id="WP_094309310.1"
                     /translation="MSNKEKQMNLLSDKNVAIIGGGPVGLTMAKLLQQNGIDVSVYERD
                     NDREARIFGGTLDLHKGSGQEAMKKAGLLQTYYDLALPMGVNIADEKGNILSTKNVKPE
                     NRFDNPEINRNDLRAILLNSLENDTVIWDRKLVMLEPGKKKWTLTFENKPSETADLVII
                     ANGGMSKVRKFVTDTEVEETGTFNIQADIHHPEVNCPGFFQLCNGNRLMAAHQGNLLFA
                     NPNNNGALHFGISFKTPDEWKNQTQVDFQNRNSVVDFLLKEFSDWDERYKELIRVTSSF
                     VGLATRIFPLGKSWKSKRPLPITMIGDAAHLMPPFAGQGVNSGLMDALILSDNLTNGKF
                     NSIEEAIENYEQQMFIYGKEAQEESTQNEIEMFKPDFTFQQLLNV"
                     /name="tetracycline-inactivating monooxygenase Tet(X4)"
     ARG             complement(3156..4309)
                     /name="tet(X4)"
                     /gene="tet(X4)"
                     /gene_name="tetracycline-inactivating monooxygenase
                     Tet(X4)"
                     /tool="amrfinderplus"
                     /drug_class="TETRACYCLINE"
                     /identity="100.0"
                     /coverage="100.0"
ORIGIN
        1 aaattgtttc ttgccgcaca ttaattctgc accctgaatt aaatagttta ccacactgtc
       61 ttcatttgac caatcgactg tgcctgcttt accatggaaa tctaaaatac gtgtgtccat
      121 ctcaggaata gttgggtccg agtctcccca agggcctgta gacataagtg ttaatgagct
      181 aactctatcg gcaaacttta tagctgctat ttgtgtaatt agcccaccta atgacatacc
      241 cacaaaatgt gctttgtcta tttcatagcc gtccaaaatt gcaatggcat catttgttaa
      301 gtcaacaatg tcgtatggtg ctgaacccgg ctcataatta gtggattttc ctacatctct
      361 gttgtcgtaa cgaataacaa aaaatccttt ttcagataat tgttggcaaa attcagtgtc
      421 ccaatacagc attgatacgg ttgcacctgc taccaaaagg attgctggat ttttcttatt
      481 tccaaaactt tccgtacaga gttcaatgcc gtttgtttta attattttct ctttcatttc
      541 tgttttcctt tgtttgcaac tgattattat cagtcctaaa attaatatcc aaagtagttt
      601 tttttcattt atcaatgttt aactgttatg ctggtatctt tcacaatgcc cgctaactta
      661 tatatatacg aaacattcta ctctatttca tacccatatg gcaagatagg cgaatgtttt
      721 tactatttta tttcgcattt tgaatttctc aaatataaaa attattttaa cattttagta
      781 cttatagtgc ttaattattt atgtttcaaa tcttatgaaa tcatataata tataaaaata
      841 tatgtatata taaatatatt aaagttgtgt caaatgttaa aatttaaaat taacagaaaa
      901 aggagtttat agttagtaaa aaatttataa cttgggtttt gaaaaagaaa atccatgaaa
      961 aagaaattaa tttatatgtc gatagcgacc tttgctatcg cacagagttc tattgctcag
     1021 aaccttgatt tacagacacc agcaaacaat cttaagcaac aaatttcatc aatatttcct
     1081 attgacgtat aggaagaata aacacccttt tcacccaagt ccaacagctt tggaccgcag
     1141 ttgactcttt cgacacccct gcgatgcaac ccaatccggc tgacggggag ccagcaacgc
     1201 tgaaaattta ccctcctctt tcccactagc ggctcctttt ccgacaacca gcacggcgga
     1261 tccctgccgc ggcgctgtga acgcagcatt ttgattggta tcgttggcct tcaggctcgt
     1321 cagtcaaaca gacccaggag cagctcagcc ggtggcgccc ggctttcggg taacgccctg
     1381 gtcccgctgg tttcggcttt gtgcttcagg tgatcaagga tctgcttgat cactataggg
     1441 tcttcaatgc aggcgatgac tttcatggcg ccgccgcagc cgctgcaggt ctcgatgtcg
     1501 atattgaaaa cacgcttgag ccgttgcgcc catgtcatcg acgctcgccg ttgtgctggt
     1561 gttgccggtt catcagccac cctgaccttg ttgcccctgc cccgttttgc cggcgtgacc
     1621 aacgcccggt gccgactgtt gggtgcgaac accccgtgga agcgggttag gttgactctg
     1681 ggcttcggta ccagggcggc cagccttgca atgaaatcca atggttcgaa aatgacgtgc
     1741 gtggtgccgt cccggtacgg cgtcttgagc tggtagcgca cgttgccgcc tcgtgttaac
     1801 gacagccgct tctcggatac cgccgggcgg ctgatgtacc ggcacagccg ttcgagcttc
     1861 ttgcgttcat cggccctggc cgccacgccg gcgtgcaggc tggacccggc taccttgcca
     1921 atcccgtcac cgaacggatc accactggtc ggcagagttt gcaaagtgaa cacctttcgc
     1981 cccgcctgtg aaccgacagc gatacggtaa gtgatcgagt gccccagcag gggtgtcatc
     2041 gggtcgtcat ccaccgcatc cgaggccaga tagctgtttt cgacatcccg ttccagcagg
     2101 ccttgccgtt ccagatagcg acccacccgg tgggcgatgg tgtgcgtcag ctgggtgagc
     2161 tctgggctgg tcggcgcctt gacccagcgg aaacgcgctg agccgtggga ttgctcgaca
     2221 tacacaccgt cgagaaacag catgtggaag tgaacattca gattgagcgc cgatccaaaa
     2281 cgctggatca gggtgaccgc gcccgtcttg gccacttggt gggtatggcc cgctttcttg
     2341 accaggtgcg tggcaatgac gcggtaaacg atgcccagca cccaccccat gatctcgggc
     2401 cggctggcaa acaggaaacg cagctgaaac gggaagctca acacccactg acgcatgggt
     2461 tgttcaggca gtacttcatc aaccagcaag gcggcacttt cggccatccg ccgcgcccca
     2521 cagctcgggc agaaaccgcg acgcttacag ctgaaagcga ccaggtgctc ggcgtggcaa
     2581 gactcgcagc gaacccgtag aaagccatgc tccagccgcc cgcattggag aaattcttca
     2641 aattcccgtt gcacatagcc cggcaattcc tttccctgct ctgccataag cgcagcgaat
     2701 gccgggtaat actcgtcaac gatctgatag agaagggttt gctcgggtcg gtggctctgg
     2761 taacgaccag tatcccgatc ccggctggcc gtcctggccg ccacatgagg catgttccgc
     2821 gtccttgcaa tactgtgttt acatacagtc tatcgcttag cggaaagttc ttttaccctc
     2881 agccgaaatg cctgccgttg ctagacattg ccagccagtg cccgtcactc ccactcaata
     2941 gttggcacaa agtcctattc taggcactac cattacttta caacgcctga agaaaagagg
     3001 atatgtttcc ttaactgaat tacatttaca acttaaccca tctctttgcg aaccgccgag
     3061 tacgtgaccc gtacgctcgg tggtgtgaga ggcgcactcc gtcagttact ggcggagccg
     3121 tctactcgat tatgtgccgt tttattccat tttatacatt taacaattgc tgaaacgtaa
     3181 agtcgggttt aaacatttca atttcgtttt gagttgattc ttcttgtgct tctttgccat
     3241 agataaacat ttgctgttca taattttcaa tagcctcttc aatgctgtta aatttcccat
     3301 tggtcagatt atccgacaat atcaaggcat ccatcaaccc gctgtttacg ccttgtcctg
     3361 caaaaggagg catcaaatga gcagcatctc caatcatcgt tatgggtaat ggacgcttac
     3421 ttttccaaga cttacctaag ggaaatattc gtgtcgctaa ccctacaaaa gatgatgtca
     3481 cacgaatcag ttctttgtag cgttcgtccc aatcggaaaa ttctttcaga agaaaatcaa
     3541 cgacactatt tctgttttga aaatctacct gcgtttggtt tttccattca tcaggtgttt
     3601 taaaacttat tccaaaatgc aatgcaccat tattattagg attcgcaaat aataaattac
     3661 cttgatgagc agccattagc cggtttccat tgcatagctg aaaaaatcca ggacagttca
     3721 cctctggatg atgaatatcg gcttgtatat tgaaagtacc tgtttcttca acttccgtgt
     3781 cggtaacaaa ttttcttact ttagacattc caccattggc aataataacc agatctgctg
     3841 tttcactcgg tttattctca aaagttagtg tccacttctt cttaccaggt tcaagcataa
     3901 caagttttct atcccaaata accgtgtcgt tttctaaact attcaacaag atagccctta
     3961 agtcatttct gtttatttca ggattgtcaa atcgattttc gggctttaca ttttttgtgg
     4021 ataaaatatt gcctttttca tcagcaatat ttacacccat tggtaaggct aagtcataat
     4081 aagtttgtaa caatcccgct tttttcattg cttcctgacc tgaacctttg tgtaggtcaa
     4141 gggttccacc aaaaattctt gcctctcggt cgttgtctct ttcgtaaact gaaacgtcta
     4201 tgccgttttg ctgtaataat tttgccatag tcagtccaac gggtccacca ccaattattg
     4261 caacgttctt atcactaagt aaattcattt gtttttcttt attgctcatt tatatgtttt
     4321 tcaattccgt caattattgt tgtccaatct tcaaagtgca attcgtgtcc tgttccttca
     4381 agagtaatta atttcgtatt ttgtattttc tcaattaata caccagcgtt tttatagtgc
     4441 caaattttgt catctgttcc gtgaattatc aaggttggtt gatttacttc atttagtcta
     4501 ttccaatatt cttcactacc ttgcaatgta gcgtgattga acatacttat ataattgttt
     4561 gctctattga actcagctct tatcagcttt tcacttcttt gtttatc
//
