LOCUS       NZ_CP123594             4367 bp    DNA     circular CON 14-AUG-2023
DEFINITION  Escherichia coli strain DJH_183sputum plasmid pDJH_Plas4, complete
            sequence.
ACCESSION   NZ_CP123594
VERSION     NZ_CP123594.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN34121641
            Assembly: GCF_030708395.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4367)
  AUTHORS   Guo,J., Duan,R., Zhang,D., Zhang,P., Qin,S., Fang,Y., Sun,Y., Lu,L.,
            Jing,H., Wang,X., Jiang,R. and Kan,B.
  TITLE     Persistent Urinary Tract Infection in Association with
            Community-Acquired NDM-5 Escherichia coli Clonal Group Following
            COVID-19 Infection - Beijing Municipality, China, 2023
  JOURNAL   China CDC Wkly 5 (26), 565-571 (2023)
   PUBMED   37457852
REFERENCE   2  (bases 1 to 4367)
  AUTHORS   Duan,R., Wang,X. and Guo,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-APR-2023) Emergency Response, National Institute for
            Communicable Disease Control and Prevention, China CDC, Changbai
            Street 155, Changping District, Beijing 102206, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. 4.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 417.68x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 08/11/2023 07:44:36
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,755
            CDSs (total)                      :: 4,634
            Genes (coding)                    :: 4,397
            CDSs (with protein)               :: 4,397
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 237
            CDSs (without protein)            :: 237
            Pseudo Genes (ambiguous residues) :: 0 of 237
            Pseudo Genes (frameshifted)       :: 73 of 237
            Pseudo Genes (incomplete)         :: 154 of 237
            Pseudo Genes (internal stop)      :: 41 of 237
            Pseudo Genes (multiple problems)  :: 30 of 237
            Pseudo Genes (short protein)      :: 4 of 237
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP123594.1.
            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..4367
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="DJH_183sputum"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pDJH_Plas4"
                     /geo_loc_name="China"
                     /collection_date="2022"
     gene            complement(join(2289..4367,1..63))
                     /locus_tag="QFB78_RS23415"
     CDS             complement(join(2289..4367,1..63))
                     /locus_tag="QFB78_RS23415"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_305769104.1"
                     /translation="MRSRKPNSAGTPSWQGRLNSPVDDAVILTPANAPSWCGDRSVLWN
                     AVEKAEQRRNSQLAREIELAIPREISREAAREAVLAFVRENFVSRGMIADVAFHHMDRT
                     NPHAHIMLTTRAVGETGFAGKVRDWNDRALAETWRASWADHANRALANAGYQEEIDHRS
                     YERQGLEKAPGLHLGKAACAMEKRGMETERGEQNRLINSLNLEIQVSRTRLAVIQVQEN
                     VRKRELSDAARRAAEALNLTIPAANASADTLREFIATLPQECGNAWEMTPEFVAMNGKA
                     NDIKREGNALVKERDILEKEMTGLRKARPVASILSELPLMTWAEPEYRKRQLRFWKLEK
                     QIESLLRTYRAVKERDIPVRRQAFETQWNTWISPGMAELKEKLSAREAERRREEAEAEA
                     RRKEQEYDARLKHHDNHRLSRETALAGVITELGRAREPGTGRITRYMMLSNRAGEFTVW
                     GDELAHYPQSVHDPVNVYLSPGGAVMVSDIREGMPESHETMARPERVRMYSGATVRHVL
                     EQMRQGWPSYGFPALPHHWPDNFYFSDDRRPAASPLPSAHRVDVTAYAAPEQLMPVVFS
                     TERNSRTLNLLLCKGPEEMLVGFVRLEDELRPVLALPSPDYSHLMVSIITENGIHLAGY
                     GEAINRDADTPYPPEPKLMQFRLKGCQDTLFAAINKPEEMPDYLFRQLGFNQTWHEWKR
                     DEQHRQQQRRPGHYRGMSM"
                     /name="MobA/MobL family protein"
     gene            complement(<2..274)
                     /locus_tag="QFB78_RS23420"
                     /pseudo=""
     CDS             complement(<2..274)
                     /locus_tag="QFB78_RS23420"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001029330.1"
                     /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="MobA/MobL family protein"
                     /name="MobA/MobL family protein"
     gene            453..728
                     /locus_tag="QFB78_RS23425"
     CDS             453..728
                     /locus_tag="QFB78_RS23425"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091757.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_052995416.1"
                     /translation="MSRTLEQKIAEAEARLQRLKAKSRSLDTAQKVIVGAAMLARVRRP
                     EEAQLRAFLLQFLRKEVTRQADVNRLQPLINELEKLPRPPAKPQNG"
                     /name="hypothetical protein"
     gene            complement(934..1842)
                     /locus_tag="QFB78_RS23430"
     CDS             complement(934..1842)
                     /locus_tag="QFB78_RS23430"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009440807.1"
                     /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_058657849.1"
                     /translation="MSAALQYFEENLPHRPYHTDDPAFGLRISGKGRALLARYIQQNQP
                     HAQHWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNLAVRTAPDASVKV
                     LKYAAAIERALCEKLDADVNYSGLICKNPFHLEWQVMEWREEAYTLDELADYLDLSASE
                     RRSVDKHYGLGRNCHLFEITRKWAYRAIRQGWPAFSQWLDAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRKFSPEGFSAVQAARGRKGGLAKGEAYEDKRFMALCMLENGYSQ
                     KAIAAMLDVHRNTIRNWAMHK"
                     /name="replication initiation protein"
     Typing          2..275
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.49e-141"
     Typing          276..446
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.512"
                     /coverage="97.0"
                     /evalue="1.23e-74"
     Typing          4151..4367
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="7.220000000000003e-110"
     Typing          complement(1115..1842)
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.376"
                     /coverage="94.0"
                     /evalue="0.0"
     Typing          complement(2293..4367)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.63"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tggcgagttc aatctccctt gccagctggg agttccggcg ctgttcggct ttctcgaccg
       61 cattccagag aacggaacgg tcaccacacc aggacggtgc attcgcaggg gtgagaatga
      121 ccgcatcatc aacgccgcgt ttacgggtgt aatcgtggat taatccggta cggtcatcgg
      181 gtatgacaga gccggaacgg taggcagcag aagcaacggc actgtagccg ttttttcgcg
      241 aaatgatttt catgctgaga tgataaatcg ccatttctgc cgtaatgcct ttttgccgtt
      301 ttctttcagc cccgcagggc gcacacaatc gaaacgaagt gaagattgta taagtgcgca
      361 cttcgtgata tgccgtgcat tatgccagct cagtttttaa actaccagtg acgagctaaa
      421 atgcgatttt tcaccgcgca aggagtcacg aaatgagcag aacactcgaa cagaagattg
      481 ctgaagctga ggccagattg cagcgcctga aggcgaagag ccggagcctg gacactgcgc
      541 aaaaagtcat tgtgggagca gccatgctgg cgagggtacg gaggccggaa gaggcgcaac
      601 tgcgtgcgtt cctgctccag ttcctgcgaa aggaagtcac aagacaggcc gatgtgaacc
      661 ggctacaacc actgattaac gagctggaga agctaccaag accacctgcg aaaccgcaga
      721 acggataagc cccggcgcgt aagtgccaca tgcaccaccg gacgcctttg cgcttcctcg
      781 cacattcgct cgctacgctc ggtcatgagg ctgcggcgag cgctaccacc gcaatcacga
      841 ggaaaccagc gccattgctg ggcggaaccg gaaaaaccgc aggaacgcca acagctcaaa
      901 aaagcgccga aaaggcgctg ttatctgata aggctatttg tgcattgccc aattacggat
      961 cgtatttcga tgtacatcca gcatcgccgc aatagctttc tgagaatatc cattctccag
     1021 catacatagc gccatgaaac gcttgtcctc gtaggcttcg cctttagcaa ggccaccttt
     1081 ccggcctcga gcggcctgta cagcggaaaa gccttccggt gagaattttc tgtgcgtgta
     1141 tttcgcaatg ctcttgccaa tagcccggca ttcagccagt gaaagaggaa cgggaagcga
     1201 tgcgttgtac atttcgacac gctggatcac ggcatcaagc cactgtgaga atgctggcca
     1261 tccctgacga atcgctctgt aagcccattt acgcgttatt tcgaacaggt ggcagtttcg
     1321 ccccagcccg taatgtttat cgacgctacg acgctctgag gcgctcaaat cgagataatc
     1381 agccagttca tcgagggtat aggcttcctc gcgccactcc atcacctgcc attccaggtg
     1441 gaacggattt ttgcaaatca gtccgctgta gttcacatct gcgtcaagtt tctcacacag
     1501 cgcacgttca attgcagcgg cgtatttcag caccttaacc gacgcatcag gcgcggttct
     1561 cacggcaaga ttgagcgcgt atagcaggtg agcgtgccca ttcacgggat tttttacggt
     1621 gatgttcggc gcgggggcgt tccggtcgct ccagtcaatc gcagccccct cgcggtcaac
     1681 gtcaaaaacc agccagtgtt gcgcatgtgg ctggttctgc tgaatgtacc gcgcaagaag
     1741 cgcacgccct ttgccggaga tgcgaaggcc gaaagcggga tcatccgtgt gatagggacg
     1801 gtgaggtaaa ttttcttcga agtattgaag cgcggcgctc atgtgttacg attccttcca
     1861 ggttatcgac cgacatcgcc cctgtatctt cgtgaaagtc ttggcggatc tacacgaatt
     1921 tcaggggcgt ttgtttttca gtcgcttaca ctacacccaa cggcaaatcc tgtcgatcct
     1981 tcccgaaaaa ccgatccatt taccataact cctgttgtac gtacccctta aaacgctctc
     2041 agacgcgttc tgacgcaaaa aacacaaaaa gacaagaaaa caccaggcca aaccagaaaa
     2101 acgcgtcaga atcgttttca ggggtctgca taactattca cgaaagcgat gcgcgatcgg
     2161 tttcgaccgt tcagaagcgc gaacgggtca aaacggcaaa ctttctcatc cagaaaacgc
     2221 ctcacgggac gcggaatttt ttcgtgtccc gtgagacgtt ggcggggttc ggggtgcagc
     2281 cccggatatc acatactcat gccccggtaa tgtccggggc gtcgttgttg ttgcctgtgc
     2341 tgttcgtccc gcttccattc atgccaggtc tgattaaatc cgagttgacg gaagagataa
     2401 tccggcatct cttccggttt gttgatggca gcaaaaagcg tgtcctgaca gcccttaagc
     2461 ctgaactgca tcagcttcgg ttccggtggg tacggagtat cagcatcacg gtttatggcc
     2521 tcaccgtagc ctgccaggtg tatcccgttc tctgtgatga tgcttaccat cagatgactg
     2581 taatccggcg acggaagcgc aagaacggga cgcagctcgt cctccaggcg cacaaaaccg
     2641 acaagcattt cctccggccc tttgcacaac agcagattca gcgtcctgct gtttcgctct
     2701 gtcgaaaaga caacgggcat gagttgctcc ggtgccgcat aagcggtgac gtccacccgg
     2761 tgcgctgacg gcagcggaga ggctgcgggc ctgcggtcgt cgctgaaata aaaattatcc
     2821 ggccagtgat gcggcagcgc cggaaaaccg taagagggcc acccctggcg catctgttcc
     2881 agtacatgcc ggaccgtcgc accggaatac attctcacac gctcaggccg cgccatcgtc
     2941 tcatgagatt ctggcattcc ctcacgtata tccgagacca tcacagcccc gcctggcgac
     3001 aggtaaacat tcaccgggtc atgaacactc tgggggtaat gcgccagctc atcaccccat
     3061 accgtgaatt ctccggctct gttactcagc atcatgtagc gggttatcct gcccgttccc
     3121 ggctctctgg cacgccccag ctccgtaata accccggcta atgccgtttc tcggctcagg
     3181 cgatggttat catggtgttt cagccgtgcg tcatattcct gttccttccg gcgcgcttcc
     3241 gcttcggctt cctccctgcg ccgctccgct tcccgtgctg acagtttttc tttcagctct
     3301 gccattcccg gcgaaatcca cgtattccac tgcgtttcaa aggcctgacg acggacggga
     3361 atgtcccgtt ctttcacggc cctgtaggtg cggagaagag attcaatctg tttctcgagt
     3421 ttccagaagc ggagttgtct tttgcggtat tccggttcag cccatgtcat caggggaagc
     3481 tctgacagga tggacgctac cggacgggct tttctgagtc cggtcatctc tttttcgaga
     3541 atatcccgct ctttcaccag cgcattcccc tcacgtttga tgtcgtttgc cttcccgttc
     3601 atcgccacga actccggtgt catctcccat gcgttcccgc attcctgcgg cagtgtggca
     3661 atgaattccc gcagggtatc cgctgaggca ttcgcggcgg gaatggtcag attaagggct
     3721 tccgctgcac gacgtgcggc atcgctgagt tcccgtttcc gcacgttctc ctgtacctgg
     3781 atgactgcca gccttgtgcg ggaaacctgt atttccaggt taaggctgtt aatcaggcgg
     3841 ttctgctcac cgcgttctgt ttccatgccc cgtttttcca tcgcacaggc agcctttccg
     3901 aggtgaaggc ccggcgcttt ctccagtccc tgacgctcgt atgaacgatg gtctatctct
     3961 tcctggtagc cggcgttcgc aagcgctctg ttcgcatggt cagcccatga tgcgcgccac
     4021 gtctcggcga gtgcccggtc gttccagtcc ctgacctttc ctgcgaatcc cgtttccccg
     4081 acagctctcg tggtcagcat gatgtgtgca tgggggttgg tccggtccat atgatggaac
     4141 gccacatcgg caatcatgcc ccgactgaca aagttttccc ggacaaaagc gagaacggcc
     4201 tcccgtgcgg cctcgcggga aatctcacgg ggaatggcga gttcaatctc ccttgccagc
     4261 tgggagttcc ggcgctgttc ggctttctcg accgcattcc agagaacgga acggtcacca
     4321 caccaggacg gtgcattcgc aggggtgaga atgaccgcat catcaac
//
