LOCUS       NZ_CP141203             4064 bp    DNA     circular CON 31-JAN-2024
DEFINITION  Escherichia coli strain WGS1363 plasmid unnamed3, complete sequence.
ACCESSION   NZ_CP141203
VERSION     NZ_CP141203.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN29499981
            Assembly: GCF_024199045.2
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4064)
  AUTHORS   Andreasen,M.R., Rick,T., Alexandersen,N.R., Hansen,K.H.,
            Pedersen,M.S., Warweitzky,J.K., Botelho,C.M., Haussler,S.,
            Jelsbak,L. and Schonning,K.
  TITLE     Identification of a CTX-M-255 beta-Lactamase containing a G239S
            Substitution Selectively Conferring Resistance to
            Penicillin/beta-Lactamase Inhibitor Combinations
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4064)
  AUTHORS   Pedersen,M.S. and Schonning,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-DEC-2023) Department of Clinical Microbiology,
            Copenhagen University Hospital, Rigshospitalet, Henrik
            Harpestrengsvej 4A, Copenhagen 2100, Denmark
REFERENCE   3  (bases 1 to 4064)
  AUTHORS   Andreasen,M.R., Hansen,K.H., Jelsbak,L., Pedersen,M.S., Mollerup,S.
            and Schoenning,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-JUL-2022) Department of Science and Environment,
            Roskilde University, Universitetsvej 1, Roskilde 4000, Denmark
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.9
            Assembly Name                     :: E.coli_WGS1363
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 80.0x
            Sequencing Technology             :: Illumina MiSeq; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/31/2024 01:49:10
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,038
            CDSs (total)                      :: 4,925
            Genes (coding)                    :: 4,684
            CDSs (with protein)               :: 4,684
            Genes (RNA)                       :: 113
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 241
            CDSs (without protein)            :: 241
            Pseudo Genes (ambiguous residues) :: 0 of 241
            Pseudo Genes (frameshifted)       :: 92 of 241
            Pseudo Genes (incomplete)         :: 175 of 241
            Pseudo Genes (internal stop)      :: 40 of 241
            Pseudo Genes (multiple problems)  :: 58 of 241
            Pseudo Genes (short protein)      :: 3 of 241
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP141203.1.
            Bacteria and source DNA available from Lotte Jelsbak, Department of
            Science and Environment, Roskilde University, Roskilde, Denmark.
            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..4064
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="WGS1363"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="unnamed3"
                     /geo_loc_name="Denmark:Copenhagen"
                     /lat_lon="55.67 N 12.57 E"
                     /collection_date="2020"
                     /collected_by="Hospital"
     gene            complement(join(3963..4064,1..591))
                     /locus_tag="NLM83_RS00005"
                     /old_locus_tag="NLM83_00005"
     CDS             complement(join(3963..4064,1..591))
                     /locus_tag="NLM83_RS00005"
                     /old_locus_tag="NLM83_00005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /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_044326273.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCISRLKSGADAELQKT
                     MTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKNDEKREEFRWIQYRAQYAKG
                     EAKARITFSDAVMPYLTQLKGQFTRVVIKNISGLSSSYSIRIYEFLQQFRCTGERIIAL
                     NDFRSMLGIENKYKQFRDLNKILIKPCVDELNKKSDLAVTVETIKKGRTVVALHFRFKE
                     DKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(1123..1377)
                     /gene="mobC"
                     /locus_tag="NLM83_RS00010"
                     /old_locus_tag="NLM83_00010"
     CDS             complement(1123..1377)
                     /gene="mobC"
                     /locus_tag="NLM83_RS00010"
                     /old_locus_tag="NLM83_00010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091747.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     gene            1556..3715
                     /gene="mobQ"
                     /locus_tag="NLM83_RS00015"
                     /old_locus_tag="NLM83_00015"
     CDS             1556..3715
                     /gene="mobQ"
                     /locus_tag="NLM83_RS00015"
                     /old_locus_tag="NLM83_00015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_042042005.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRNEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRTERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREVPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     Typing          complement(1379..1555)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          1556..1914
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.333"
                     /coverage="100.0"
                     /evalue="8.460000000000002e-179"
     Typing          complement(2..591)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.453"
                     /coverage="85.0"
                     /evalue="0.0"
     Typing          complement(3964..4064)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.1e-45"
     Typing          1470..3712
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.93"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttttttgttc agttcgtcaa cacagggttt tattagtatt ttatttaagt ctctgaattg
       61 tttgtattta ttttcaatcc ctaacattga acgaaagtca ttaagagcaa taattctctc
      121 tcccgtacag cggaattgct ggaggaactc gtatattctt atactgtaac tacttgataa
      181 acctgatatg ttttttataa caacgcgcgt gaattgcccc ttcagttgcg tcagataagg
      241 cattaccgcg tcagaaaagg ttattcgagc cttggcctca cctttagcgt actgtgcccg
      301 atactggatc cagcggaact cctcacgctt ctcgtcattc ttgagaatga tcgacctgtc
      361 ccataaacga tcgatcgctt cctgtaactg aacctcggca tttttccgcc ccatgtcagg
      421 gaatgaatca aaatattccg cagcggtaat ggtcattgtc ttttgcaatt cagcatcagc
      481 accagatttc aatcgactga tacacagcaa cagaaaacgt tgttcctgta gggtcaactt
      541 gtagctggcc tcaaccaaag cattcgactt gtaggcaatc aagtccgaca tacaaagatc
      601 ccgttcaaat gtggtgatgc tttaatgtgc cccacaaata agaaatgtgg aatatttttt
      661 tttatatcct cacatttctg tgaataacac cttaaattcc tccaccttta ccttaaattc
      721 ctccacctaa acaccttaaa ttcctccaca tataccttaa attcctccac atataccact
      781 gcaacatatt gattttatta atgaatttcg cccctaaaac aagtattaaa aacaagatct
      841 taaaaacaag atctaaaaac ttaacggcga gcctgtggat aacttggggt gctgaaaaca
      901 aaaaacaaat aaaaacaatg tgttgcaaga aagtagaatt gcaagttccg aatactcccc
      961 ttccaaccct gtggaaatcc agtattcatg cgggttcagc gcatatcacc tgccgaaaaa
     1021 ccgtgcgtat gtgctcaacc tggcgacgga ttcacttccg cttcctcgcc cactcgctcg
     1081 ctaacgctcg gtcgctgggg ctgcggcgag cggacgatac aatcactgtc ctggcagcgc
     1141 ctccagctcg ttaatcagcg gcagtatgcg cgtcacatca gcctgtcgtg tcacctctgc
     1201 cttcaggaac tggagtaacc aggcacgcaa ctgcacctcc tccggctttc tgacctttgc
     1261 cagcaatgct gcacccacaa caaccttctg cgctgtgtcc aagctccggc tcttcgcctt
     1321 caggcgctgt aatctcgcct cagcatcagc aatcttctgt tcgagcgttc tgctcatgat
     1381 gtaactccgt gcgcgatgaa aaatcgcatt ttagcgcgtc actggtagtt taaaaactga
     1441 gctggcataa tgcacggcaa atcacgaagt gcgcacttat acaatctcca ctccgtttcg
     1501 attgtgtgcg ccctgcgggg ctgaaagaaa actacaaaaa ggcattacgg cagaaatggc
     1561 gatttatcat ctcagcatga aaattatctc cagaagcagc ggctacagcg ccgtagcttc
     1621 cgctgcctat cgttccggtt cactgatgct tgatgagcgt accggactga ctcacgacta
     1681 cacccgcaaa agcggtgtgg ctgaagctgt gattctgacc cccgcgacag cccctgcctg
     1741 gtgtacgaac cgtgccgaac tctggaatgc cgttgagaag gccgaacgcc ggaagaactc
     1801 acaacttgcg cgggaaattg aactcgctat cccccgtgaa ctgccgcagg atgccgcacg
     1861 ggaaaccgtt ctcgcctttg tcagagaaaa ctttgtcagt cagggcatga ttgctgatgt
     1921 ggcgttccat cacatggata aaacaaatcc ccatgcgcac atcatgctga ccacgagggc
     1981 tgtcggacct gctgggttcg gcggaaaggt cagggactgg aacgaccgga cacatgccga
     2041 gacgtggcgt gcatcatggg ctgaccatgc aaacagagca ctggcgaacg ccggttatca
     2101 ggaagagata gaccatcgtt catacgagcg acaggggctt gagaaaacgc ctggtattca
     2161 cctcggaaag tctgcctgtg cgatggaaac acgcggtatc gaaacagaac gcggcgaaca
     2221 gaatcgtctg attaacaggc ttaacctgga aatacagatt tcccgcactg aactcaggaa
     2281 cagcgggctg acagagcctg cccgccgtgt ggctgacctt ctgaatatcg tgcttcctga
     2341 caacgcaact tcgtacacac tacgtgacat catcgaagcg ttgccgaagg acagtaatgc
     2401 ggcatggaaa ctcaccagta atgccatgtc gatgatggca gatatgcagg cgacgcgcag
     2461 acgctgggaa gagctgaaca ccgaacgaaa ggaagcgatg agccatgctg ccagcctgaa
     2521 aaaatcatca ccgttttcgt ccggtttttc ccgtattccc ctgatgcaat gggcggcacc
     2581 ggaataccgt aacgaacagg gaaaaattca gtcgctgagc cagcaaatgg aaaaattgcg
     2641 acagcattac cggaaggtgg agaaacagga cattcccgcg agtcagacgg catttgaaaa
     2701 acagtggcag cagtgggggg catccggcct tgcagctctc agagtccagt tgcttaaacg
     2761 tgaagaggaa ttgcgccgga aggagcagga ggatacagaa cgtagtcgca cggagcgacg
     2821 agcggaacag ctcaggaaaa atgacaatgc cgttatggat tcaggggtac tgagcgcagt
     2881 cgttacgggg tatggcgagg cccccatgcc tggtaacggg gaaatgacct gttaccttct
     2941 gcttcacaac cggaacggag aatacacgct ctgggggaac gagctggaga aataccgcac
     3001 cagaatcttt gagcgtgttg atttaatgcg tgacaggagt ggttatatct gtgaccgaag
     3061 cgaaatcggt caacatccac cactgcaacg tgtttattcc tctgcgacct ttgagcaact
     3121 tctgacgcag gtttgccaga catggccgca atatacccgc aatctccgcc agccgaagac
     3181 atggccggag tctttctgtc ttggagaaga ccgccagcca gccatgccat cactggcagc
     3241 aaggaaggtg gattttacgc agggacgtct gccaccgacg ctgatgccgg taatgagttc
     3301 tgtcgaccgg gaaacccgcc agcttcagct tttgctggtc atgggcgtgg atgactctct
     3361 gggcggtgtt gtccggctta atggtacgct gtatcccgcg tttgccgttc cctcagccga
     3421 taacagccag ctggtcatca gtgcactgac cgataagggg ttacggtatg cagggtatgg
     3481 tgttgccgta aatcacgatg cagacagcca catatcacct gcgccggaac ttatggagtt
     3541 tcatctgaaa acccgtgagg taccgctttt tgctgccgtc aacacaccag aaaaacagcc
     3601 ggatcatctg ttccgctcgc tgggtttcaa tcgtacctgg gacgaatggc ggcgcgagga
     3661 agatgcaaga acacacacca ccgagaggag acatgatcgc ggttggtcac agtgaatgtg
     3721 aacaatattt tgttttgttt aacatcgtgt tatgttcgtc gatgttcatc gacagggatg
     3781 aatgcaagaa gcacactcac ataacgcaag catagttttg tttttccgcc cccaaaaatt
     3841 gggggttctt ttttcgctgc atcagagcgt ttttggcgca atttttcact tcaatagtac
     3901 cttcgcacta ctaacacaaa aaaaacgcag cagggagcgt tttaggtgca ttaaaatcga
     3961 ttttagatcg tcatcttgat ctgtttgtct tccttgaagc gaaaatgcag ggctacaacc
     4021 gtgcgcccct ttttgatcgt ctcaaccgtt acagccaggt cgct
//
