LOCUS       NZ_CP080069             4608 bp    DNA     circular CON 16-JUN-2024
DEFINITION  Escherichia coli strain 19SZHZ803Rt plasmid p803Rt_tetX4, complete
            sequence.
ACCESSION   NZ_CP080069
VERSION     NZ_CP080069.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN20339661
            Assembly: GCF_023516055.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4608)
  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  JOURNAL   Unpublished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 4608)
  AUTHORS   Liu,B., Liu,W. and Fu,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (22-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_023516055.1-RS_2024_06_15
            Annotation Date                   :: 06/15/2024 05:07:10
            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)                     :: 4,666
            CDSs (total)                      :: 4,546
            Genes (coding)                    :: 4,387
            CDSs (with protein)               :: 4,387
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 159
            CDSs (without protein)            :: 159
            Pseudo Genes (ambiguous residues) :: 0 of 159
            Pseudo Genes (frameshifted)       :: 52 of 159
            Pseudo Genes (incomplete)         :: 101 of 159
            Pseudo Genes (internal stop)      :: 41 of 159
            Pseudo Genes (multiple problems)  :: 33 of 159
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP080069.1.
            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..4608
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="19SZHZ803Rt"
                     /isolation_source="Human feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p803Rt_tetX4"
                     /geo_loc_name="China:Shenzhen"
                     /altitude="120 m"
                     /collection_date="2019-07-13"
                     /collected_by="Bang Liu"
     gene            join(4318..4608,1..867)
                     /locus_tag="KZO14_RS23210"
                     /old_locus_tag="KZO14_23195"
     CDS             join(4318..4608,1..867)
                     /locus_tag="KZO14_RS23210"
                     /old_locus_tag="KZO14_23195"
                     /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)"
     gene            1206..2699
                     /locus_tag="KZO14_RS23215"
                     /old_locus_tag="KZO14_23200"
     CDS             1206..2699
                     /locus_tag="KZO14_RS23215"
                     /old_locus_tag="KZO14_23200"
                     /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            3411..4328
                     /gene="estT"
                     /locus_tag="KZO14_RS23220"
                     /old_locus_tag="KZO14_23205"
     CDS             3411..4328
                     /gene="estT"
                     /locus_tag="KZO14_RS23220"
                     /old_locus_tag="KZO14_23205"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014937123.1"
                     /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_094309312.1"
                     /translation="MKKKLLWILILGLIIISCKQRKTEMKEKIIKTNGIELCTESFGNK
                     KNPAILLVAGATVSMLYWDTEFCQQLSEKGFFVIRYDNRDVGKSTNYEPGSAPYDIVDL
                     TNDAIAILDGYEIDKAHFVGMSLGGLITQIAAIKFADRVSSLTLMSTGPWGDSDPTIPE
                     MDTRILDFHGKAGTVDWSNEDSVVNYLIQGAELMCGKKQFDKQRSEKLIRAEFNRANNY
                     ISMFNHATLQGSEEYWNRLNEVNQPTLIIHGTDDKIWHYKNAGVLIEKIQNTKLITLEG
                     TGHELHFEDWTTIIDGIEKHINEQ"
                     /name="estT"
     ARG             4319..4608
                     /name="tet(X4)"
                     /gene="tet(X4)"
                     /gene_name="tetracycline inactivation enzyme"
                     /tool="rgi"
                     /drug_class="glycylcycline; tetracycline antibiotic"
                     /identity="100.0"
                     /coverage="25.19"
     ARG             2..867
                     /name="tet(X4)"
                     /gene="tet(X4)"
                     /gene_name="tetracycline inactivation enzyme"
                     /tool="rgi"
                     /drug_class="glycylcycline; tetracycline antibiotic"
                     /identity="100.0"
                     /coverage="74.81"
ORIGIN
        1 acaaaaaatg taaagcccga aaatcgattt gacaatcctg aaataaacag aaatgactta
       61 agggctatct tgttgaatag tttagaaaac gacacggtta tttgggatag aaaacttgtt
      121 atgcttgaac ctggtaagaa gaagtggaca ctaacttttg agaataaacc gagtgaaaca
      181 gcagatctgg ttattattgc caatggtgga atgtctaaag taagaaaatt tgttaccgac
      241 acggaagttg aagaaacagg tactttcaat atacaagccg atattcatca tccagaggtg
      301 aactgtcctg gattttttca gctatgcaat ggaaaccggc taatggctgc tcatcaaggt
      361 aatttattat ttgcgaatcc taataataat ggtgcattgc attttggaat aagttttaaa
      421 acacctgatg aatggaaaaa ccaaacgcag gtagattttc aaaacagaaa tagtgtcgtt
      481 gattttcttc tgaaagaatt ttccgattgg gacgaacgct acaaagaact gattcgtgtg
      541 acatcatctt ttgtagggtt agcgacacga atatttccct taggtaagtc ttggaaaagt
      601 aagcgtccat tacccataac gatgattgga gatgctgctc atttgatgcc tccttttgca
      661 ggacaaggcg taaacagcgg gttgatggat gccttgatat tgtcggataa tctgaccaat
      721 gggaaattta acagcattga agaggctatt gaaaattatg aacagcaaat gtttatctat
      781 ggcaaagaag cacaagaaga atcaactcaa aacgaaattg aaatgtttaa acccgacttt
      841 acgtttcagc aattgttaaa tgtataaaat ggaataaaac ggcacataat cgagtagacg
      901 gctccgccag taactgacgg agtgcgcctc tcacaccacc gagcgtacgg gtcacgtact
      961 cggcggttcg caaagagatg ggttaagttg taaatgtaat tcagttaagg aaacatatcc
     1021 tcttttcttc aggcgttgta aagtaatggt agtgcctaga ataggacttt gtgccaacta
     1081 ttgagtggga gtgacgggca ctggctggca atgtctagca acggcaggca tttcggctga
     1141 gggtaaaaga actttccgct aagcgataga ctgtatgtaa acacagtatt gcaaggacgc
     1201 ggaacatgcc tcatgtggcg gccaggacgg ccagccggga tcgggatact ggtcgttacc
     1261 agagccaccg acccgagcaa acccttctct atcagatcgt tgacgagtat tacccggcat
     1321 tcgctgcgct tatggcagag cagggaaagg aattgccggg ctatgtgcaa cgggaatttg
     1381 aagaatttct ccaatgcggg cggctggagc atggctttct acgggttcgc tgcgagtctt
     1441 gccacgccga gcacctggtc gctttcagct gtaagcgtcg cggtttctgc ccgagctgtg
     1501 gggcgcggcg gatggccgaa agtgccgcct tgctggttga tgaagtactg cctgaacaac
     1561 ccatgcgtca gtgggtgttg agtttcccgt ttcagctgcg tttcctgttt gccagccggc
     1621 ccgagatcat ggggtgggtg ctgggcatcg tttaccgcgt cattgccacg cacctggtca
     1681 agaaagcggg ccatacccac caagtggcca agacgggcgc ggtcaccctg atccagcgtt
     1741 ttggatcggc gctcaatctg aatgttcact tccacatgct gtttctcgac ggtgtgtatg
     1801 tcgagcaatc ccacggctca gcgcgtttcc gctgggtcaa ggcgccgacc agcccagagc
     1861 tcacccagct gacgcacacc atcgcccacc gggtgggtcg ctatctggaa cggcaaggcc
     1921 tgctggaacg ggatgtcgaa aacagctatc tggcctcgga tgcggtggat gacgacccga
     1981 tgacacccct gctggggcac tcgatcactt accgtatcgc tgtcggttca caggcggggc
     2041 gaaaggtgtt cactttgcaa actctgccga ccagtggtga tccgttcggt gacgggattg
     2101 gcaaggtagc cgggtccagc ctgcacgccg gcgtggcggc cagggccgat gaacgcaaga
     2161 agctcgaacg gctgtgccgg tacatcagcc gcccggcggt atccgagaag cggctgtcgt
     2221 taacacgagg cggcaacgtg cgctaccagc tcaagacgcc gtaccgggac ggcaccacgc
     2281 acgtcatttt cgaaccattg gatttcattg caaggctggc cgccctggta ccgaagccca
     2341 gagtcaacct aacccgcttc cacggggtgt tcgcacccaa cagtcggcac cgggcgttgg
     2401 tcacgccggc aaaacggggc aggggcaaca aggtcagggt ggctgatgaa ccggcaacac
     2461 cagcacaacg gcgagcgtcg atgacatggg cgcaacggct caagcgtgtt ttcaatatcg
     2521 acatcgagac ctgcagcggc tgcggcggcg ccatgaaagt catcgcctgc attgaagacc
     2581 ctatagtgat caagcagatc cttgatcacc tgaagcacaa agccgaaacc agcgggacca
     2641 gggcgttacc cgaaagccgg gcgccaccgg ctgagctgct cctgggtctg tttgactgac
     2701 gagcctgaag gccaacgata ccaatcaaaa tgctgcgttc acagcgccgc ggcagggatc
     2761 cgccgtgctg gttgtcggaa aaggagccgc tagtgggaaa gaggagggta aattttcagc
     2821 gttgctggct ccccgtcagc cggattgggt tgcatcgcag gggtgtcgaa agagtcaact
     2881 gcggtccaaa gctgttggac ttgggtgaaa agggcgttta ttcttcctat acgtcaatag
     2941 gaaatattga tgaaatttgt tgcttaagat tgtttgctgg tgtctgtaaa tcaaggttct
     3001 gagcaataga actctgtgcg atagcaaagg tcgctatcga catataaatt aatttctttt
     3061 tcatggattt tctttttcaa aacccaagtt ataaattttt tactaactat aaactccttt
     3121 ttctgttaat tttaaatttt aacatttgac acaactttaa tatatttata tatacatata
     3181 tttttatata ttatatgatt tcataagatt tgaaacataa ataattaagc actataagta
     3241 ctaaaatgtt aaaataattt ttatatttga gaaattcaaa atgcgaaata aaatagtaaa
     3301 aacattcgcc tatcttgcca tatgggtatg aaatagagta gaatgtttcg tatatatata
     3361 agttagcggg cattgtgaaa gataccagca taacagttaa acattgataa atgaaaaaaa
     3421 aactactttg gatattaatt ttaggactga taataatcag ttgcaaacaa aggaaaacag
     3481 aaatgaaaga gaaaataatt aaaacaaacg gcattgaact ctgtacggaa agttttggaa
     3541 ataagaaaaa tccagcaatc cttttggtag caggtgcaac cgtatcaatg ctgtattggg
     3601 acactgaatt ttgccaacaa ttatctgaaa aaggattttt tgttattcgt tacgacaaca
     3661 gagatgtagg aaaatccact aattatgagc cgggttcagc accatacgac attgttgact
     3721 taacaaatga tgccattgca attttggacg gctatgaaat agacaaagca cattttgtgg
     3781 gtatgtcatt aggtgggcta attacacaaa tagcagctat aaagtttgcc gatagagtta
     3841 gctcattaac acttatgtct acaggccctt ggggagactc ggacccaact attcctgaga
     3901 tggacacacg tattttagat ttccatggta aagcaggcac agtcgattgg tcaaatgaag
     3961 acagtgtggt aaactattta attcagggtg cagaattaat gtgcggcaag aaacaatttg
     4021 ataaacaaag aagtgaaaag ctgataagag ctgagttcaa tagagcaaac aattatataa
     4081 gtatgttcaa tcacgctaca ttgcaaggta gtgaagaata ttggaataga ctaaatgaag
     4141 taaatcaacc aaccttgata attcacggaa cagatgacaa aatttggcac tataaaaacg
     4201 ctggtgtatt aattgagaaa atacaaaata cgaaattaat tactcttgaa ggaacaggac
     4261 acgaattgca ctttgaagat tggacaacaa taattgacgg aattgaaaaa catataaatg
     4321 agcaataaag aaaaacaaat gaatttactt agtgataaga acgttgcaat aattggtggt
     4381 ggacccgttg gactgactat ggcaaaatta ttacagcaaa acggcataga cgtttcagtt
     4441 tacgaaagag acaacgaccg agaggcaaga atttttggtg gaacccttga cctacacaaa
     4501 ggttcaggtc aggaagcaat gaaaaaagcg ggattgttac aaacttatta tgacttagcc
     4561 ttaccaatgg gtgtaaatat tgctgatgaa aaaggcaata ttttatcc
//
