LOCUS       NZ_CP099758             4063 bp    DNA     circular CON 29-SEP-2023
DEFINITION  Escherichia coli strain 806883-9-2019 plasmid p806883-9-2019d,
            complete sequence.
ACCESSION   NZ_CP099758
VERSION     NZ_CP099758.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN29187367
            Assembly: GCF_025232475.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4063)
  AUTHORS   Fernandez,J.E., Seth-Smith,H.M.B., Nordmann,P., Egli,A.,
            Endimiani,A. and Perreten,V.
  TITLE     Intra and inter-species spread of a novel conjugative
            multidrug-resistant IncC plasmid co-harbouring blaOXA-181 and armA
            in a cystic fibrosis patient
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4063)
  AUTHORS   Fernandez,J.E. and Perreten,V.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-JUN-2022) Institute of Veterinary Bacteriology,
            University of Bern, Laenggassstrasse 122, Bern 3012, Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: MAR-2022
            Assembly Method                   :: Unicycler v. 0.4.9b
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 38x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/29/2023 07:30:18
            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)                     :: 5,257
            CDSs (total)                      :: 5,141
            Genes (coding)                    :: 4,934
            CDSs (with protein)               :: 4,934
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 207
            CDSs (without protein)            :: 207
            Pseudo Genes (ambiguous residues) :: 0 of 207
            Pseudo Genes (frameshifted)       :: 81 of 207
            Pseudo Genes (incomplete)         :: 138 of 207
            Pseudo Genes (internal stop)      :: 38 of 207
            Pseudo Genes (multiple problems)  :: 45 of 207
            Pseudo Genes (short protein)      :: 5 of 207
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP099758.1.
            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..4063
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="806883-9-2019"
                     /isolation_source="Rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p806883-9-2019d"
                     /geo_loc_name="Switzerland: Basel"
                     /lat_lon="47.5617 N 7.58339 E"
                     /collection_date="2019"
                     /collected_by="University Hospital Basel"
     gene            complement(327..581)
                     /gene="mobC"
                     /locus_tag="NH020_RS26160"
                     /old_locus_tag="NH020_26160"
     CDS             complement(327..581)
                     /gene="mobC"
                     /locus_tag="NH020_RS26160"
                     /old_locus_tag="NH020_26160"
                     /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_000091746.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     gene            760..2907
                     /gene="mobQ"
                     /locus_tag="NH020_RS26165"
                     /old_locus_tag="NH020_26165"
     CDS             760..2907
                     /gene="mobQ"
                     /locus_tag="NH020_RS26165"
                     /old_locus_tag="NH020_26165"
                     /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_001029354.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPHELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAIGPAGFSGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNGGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPKDSN
                     SAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQMAFEKQWQQWGESGLAALRAQL
                     LKREEELRRKEQEDTERSRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRTRIFESVDLMRDRSGYICDRSEIGQRPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSPAARKVDFMQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSLGGVIRLNGTLYPAFAVPSADNRHLVISALTDKGLRYA
                     GYGVAVNHDADSHISPAPELMQFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRTWEEW
                     QREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     gene            complement(3155..3856)
                     /locus_tag="NH020_RS26170"
                     /old_locus_tag="NH020_26170"
     CDS             complement(3155..3856)
                     /locus_tag="NH020_RS26170"
                     /old_locus_tag="NH020_26170"
                     /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_001281395.1"
                     /translation="MSDLIAYKSNALIEASYKLTLQEQRFLLVCISRLKSGEDSPSPDE
                     QKTMTITAAEFHDAFPDMGRQHAEARLKEAIDRLWDRSVIIKNEEKREEFRWVQYRAQY
                     FKGEAKVDITFSDAIMPYLTQLKGQFTRVVVKNVSSLSSTYSIRIYELLQQFRSTGDRT
                     IAIDDFRTMLAVEDKYQQFKDLNKMIIKPAIAELNEKSDLVVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     Typing          complement(583..759)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          760..1118
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(3156..3856)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          674..2904
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.989"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tcatggtgtt acaagaccta aaaaggtttt aaaaaaaaag atctaaaaat aagatcttaa
       61 aaacttaacg gcgagcctgt ggataacttg gggtgctgaa aacaaaaaac caataaaaac
      121 aatgcgttgc aataaagcag aattgcaagt ttcgaataca ccccctccaa ccctgtggaa
      181 acccagtatt catgcgggtt cagcgcatat cacctgccga aaaaccgtgc gtatgtgctc
      241 aacctggcga ctgattcact tccgcttcct cgcccactcg ctcgctaacg ctcggtcgct
      301 ggggctgcgg cgagcggacg atacaatcac tgttctggca gcgcctccag ctcgttaatc
      361 agcggcagta tgcgcgtcac atcagcctgt cgtgtcacct ctgccttcag gaactggagt
      421 aaccaggcac gcaactgcac ctcctccggc tttctgacct ttgccagcaa tgcagcaccc
      481 acaacaacct tctgcgctgt gtccaggctc cggctcttcg ccttcaggcg ctgtaatctc
      541 gcctcagcat cagcaatctt ctgttcgagc gttctgctca tgatgtaact ccgtgcgcga
      601 tgaaaaatcg cattttagcg cgtcactggt agtttaaaaa ctgagctggc ataatgcacg
      661 gcaaatcacg aagtgcgcac ttatacaatc tccactccgt ttcgattgtg tgcgccctgc
      721 ggggctgaaa gaaaactaca aaaaggcatt acggcagaaa tggcgattta tcatctcagc
      781 atgaaaatta tctccagaag cagcggctac agcgccgtag cttccgctgc ctatcgttcc
      841 ggttcactga tgcttgatga gcgtaccgga ctgactcacg actacacccg caaaagcggt
      901 gtggctgagg ctgtgattct gacccccgcc accgcccctg cctggtgtac gaaccgtgcc
      961 gaactctgga atgccgttga gaaggccgaa cgccggaaga actcacaact tgcgcgggaa
     1021 attgaactcg ccatccccca cgaactgccg caggatgccg cacgggaaac cgttctcgcc
     1081 tttgtcagag aaaactttgt cagtcagggc atgattgctg atgtggcgtt ccatcacatg
     1141 gataaaacaa atccccatgc gcacatcatg ctgaccacga gggctatcgg acctgctggg
     1201 ttcagcggaa aggtcaggga ctggaacgac cggacacatg ccgagacgtg gcgggcatca
     1261 tgggctgacc atgcaaacag ggcactggcg aacgccggtt atcaggaaga gatagaccat
     1321 cgttcatacg agcgacaggg gcttgagaaa acgcctggta ttcacctcgg aaagtctgcc
     1381 tgtgcgatgg aaacacgcgg tatcgaaaca gaacgcggcg aacagaatcg tctgattaac
     1441 aggcttaacc tggaaataca gatttcccgc accgaactca ggaacggagg gctgacagag
     1501 cctgcccgcc gtgtggctga ccttctgaat atcgggcttc ctgacaacgc aacttcgtac
     1561 acactacgtg acattatcga agcgttgccg aaggacagta actcggcatg gaaactcacc
     1621 agtaatgcca tgtcgatgat ggcagatatg caggcgacgc gcagacgctg ggaagagctg
     1681 aacaccgaac gaaaggaagc gatgagccat gctgccagcc tgaaaaaatc atcgccgttt
     1741 tcgtccggtt tttcccgtat tcccctgatg caatgggcgg caccggaata ccgtagtgag
     1801 cagggaaaaa tccagtctct gagccagcaa atggaaaaat tacgacagca ttaccggaag
     1861 gtggagaaac aggacattcc cgcgagtcag atggcatttg aaaaacagtg gcagcagtgg
     1921 ggggaatccg gccttgcagc tctcagagcc cagttgctta aacgtgaaga ggaattgcgc
     1981 cggaaggaac aggaagatac tgaacgtagt cgcgcggagc agctcaggaa aaatgacaat
     2041 gccgttatgg attcaggggt gctgagagca gtcgttacgg ggtatggcga ggctcccatg
     2101 cctggtaacg gggaaatgac ctgttacctt ctgcttcaca accggaacgg agaatatacg
     2161 ctctggggga acgagctgga gaaataccgc accagaatct ttgagagtgt tgatttaatg
     2221 cgtgacagga gtggttatat ctgtgaccga agcgaaatcg gccaacgtcc gccactgcaa
     2281 cgtgtttatt cctctgcaac ctttgagcaa ctgctgacgc aggtttgcca gacatggccg
     2341 caacataccc gcaatctccg ccagccgaag acatggccgg agtctttctg tcttggagaa
     2401 gaccgccagc cagccatgcc atcaccagcg gcaaggaagg tggattttat gcagggacgt
     2461 ctgccaccga cgctgatgcc ggtcatgagt tctgtcgacc gggaaacccg ccagcttcag
     2521 cttttgctgg tcatgggcgt ggatgactct ctgggcggtg ttatccggct taatggtacg
     2581 ctgtatcccg cgtttgccgt tccctcagcc gataacaggc atctggtcat cagtgcgctg
     2641 accgataagg ggttacggta tgcagggtat ggtgttgccg taaatcacga tgcagacagc
     2701 cacatatcac ctgcaccaga actgatgcag tttcatctga aaacccgtga ggcaccgctt
     2761 tttgctgccg tcaacacacc agaaaaacag ccggatcatc tgttccgctc gctgggtttt
     2821 aatcgtacct gggaggaatg gcagcgcgag gaagatgcac gaacacacac caccgagagg
     2881 agacatgatc gcggttggtc acagtgaatg tgaacaatat tttgttttgt ttaacatcgt
     2941 gttatgttcg tcgatgttca tcgacaggga tgaatgcaag aagcacactc acataacgca
     3001 agcatagttt tgtttttccg cccccaaaaa ttggggggtc ttttttcgct gcatcagagc
     3061 gtttttgacg caatttttca cttcaatagt accttcgcac tactaacaca aaaaaaacgc
     3121 agcagggagc gttttaggtg ccttaaaatc gattttagat cgtcatcttg atctgtttgt
     3181 cttccttgaa gcgaaaatgc agggctacaa ccgtgcgccc ctttttgatc gtctcaacag
     3241 ttacaaccag atcgcttttt tcgttcagtt cggcgatggc tggcttgatt atcatcttat
     3301 tcaagtcttt gaattgttga tatttatctt caacggcaag catggttcgg aaatcatcga
     3361 tagctatcgt tctgtcaccg gtgctgcgga actgctggag cagctcgtaa atgcggatgc
     3421 tgtaggtgct ggaaaggctg gagacgttct tcacgactac ccgcgtaaac tgccccttga
     3481 gctgtgtcag atacggcatg atggcatcgg agaaggtgat atctactttc gcctcacctt
     3541 tgaaatactg cgcccggtac tgcacccagc ggaactcttc tcgtttttcc tcgttcttga
     3601 tgattactga cctgtcccag aggcgatcta tcgcttcctt gagcctagct tcagcgtgct
     3661 gccgtcccat gtcaggaaag gcatcatgaa actctgcagc cgtgatggtc atggtttttt
     3721 gttcatccgg cgaaggggaa tcttctccgg attttaggcg gctgatacag accagcagga
     3781 agcgctgttc ctgcaaagtg agcttgtagc ttgcctcgat aagggcgttt gatttgtaag
     3841 ctatcagatc tgacatttcg cttgctcgtt gctattggtg gcgttttttt actgtacgcc
     3901 acttatcata tgggtggaag tttttttttt gcaaccccct ttttctgtgg attacacccc
     3961 caaaagctcc acctttcacc cccaaaagct ccacctttca cccccaaaag ctccaccttt
     4021 cacccccaaa agctccactt atcttgccag aacatcttta aaa
//
