LOCUS       NZ_CP082079             4629 bp    DNA     circular CON 23-JUL-2023
DEFINITION  Escherichia coli strain MS20657 plasmid pMS20657B, complete
            sequence.
ACCESSION   NZ_CP082079
VERSION     NZ_CP082079.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN20934295
            Assembly: GCF_030515435.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4629)
  AUTHORS   Nhu,N.T.K., Phan,M.-D., Brauner,A., Westerlund-Wilkstrom,B.,
            Irwin,A.D. and Schembri,M.A.
  TITLE     Neonatal meningitis Escherichia coli
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4629)
  AUTHORS   Nhu,N.T.K., Phan,M.-D., Brauner,A., Westerlund-Wilkstrom,B.,
            Irwin,A.D. and Schembri,M.A.
  TITLE     Direct Submission
  JOURNAL   Submitted (23-AUG-2021) School of Chemistry and Molecular
            Biosciences, University of Queensland, Building 76 Cooper road,
            Brisbane, Queensland 4072, Australia
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: MAY-2021
            Assembly Method                   :: flye v. 2.5
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 180x
            Sequencing Technology             :: Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/21/2023 17:16:12
            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)                     :: 4,872
            CDSs (total)                      :: 4,755
            Genes (coding)                    :: 4,531
            CDSs (with protein)               :: 4,531
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 224
            CDSs (without protein)            :: 224
            Pseudo Genes (ambiguous residues) :: 0 of 224
            Pseudo Genes (frameshifted)       :: 96 of 224
            Pseudo Genes (incomplete)         :: 110 of 224
            Pseudo Genes (internal stop)      :: 60 of 224
            Pseudo Genes (multiple problems)  :: 34 of 224
            Pseudo Genes (short protein)      :: 3 of 224
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP082079.1.
            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..4629
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="MS20657"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMS20657B"
                     /geo_loc_name="Finland"
                     /collected_by="Benita Westerlund-Wilkstrom"
                     /genotype="ST567"
     gene            complement(297..1136)
                     /locus_tag="K6125_RS24335"
                     /old_locus_tag="K6125_24170"
     CDS             complement(297..1136)
                     /locus_tag="K6125_RS24335"
                     /old_locus_tag="K6125_24170"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354646.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001354646.1"
                     /translation="MLTLFIFFVLLIAACFFCFAPPRRGYDRNEIIPYKIKLSINKYRL
                     YIYSSGKVRQYLLFLVILSLYYSIAEPFKSELIKNISYSLMAAFIFDTGLNFSKENITK
                     GVISTRWHNDLYSSFERMKAINKIYYPSNKEINTEGLSKAITSSLFNDDANSFAKRDFR
                     LMWDLSSEKYLSYKEIIIRKGDKLDAVCLRFINDDYKFLVNFNRDEEVFKYFPSIMQPS
                     LKTYRALSRLVNSIKDPSRFKFTTESLEMELLEYLELRNELFNDIEEVMGSYAQRAP"
                     /name="hypothetical protein"
     gene            complement(2147..2338)
                     /locus_tag="K6125_RS24340"
                     /old_locus_tag="K6125_24175"
     CDS             complement(2147..2338)
                     /locus_tag="K6125_RS24340"
                     /old_locus_tag="K6125_24175"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_000165986.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2436..2760
                     /locus_tag="K6125_RS24345"
                     /old_locus_tag="K6125_24180"
                     /pseudo=""
     CDS             2436..2760
                     /locus_tag="K6125_RS24345"
                     /old_locus_tag="K6125_24180"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2969..>3403
                     /locus_tag="K6125_RS24350"
                     /pseudo=""
     CDS             2969..>3403
                     /locus_tag="K6125_RS24350"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            3438..3998
                     /locus_tag="K6125_RS24355"
                     /old_locus_tag="K6125_24190"
     CDS             3438..3998
                     /locus_tag="K6125_RS24355"
                     /old_locus_tag="K6125_24190"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_000067488.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKQQLDTLSTTVSTQLSTTEAELSRQQKNLLWQVIKGRVLFPALTA
                     LSVTGGIFLGCWGLIQWQESRIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            4005..4238
                     /locus_tag="K6125_RS24360"
                     /old_locus_tag="K6125_24195"
     CDS             4005..4238
                     /locus_tag="K6125_RS24360"
                     /old_locus_tag="K6125_24195"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137388.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHAVTQQNNA
                     ILNERVVNLSQQVQLLAGQVDRLSRLFITNNR"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          1975..2059
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.03e-37"
     Typing          complement(1406..1964)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.761"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2404..2741
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="83.186"
                     /coverage="96.0"
                     /evalue="4.7599999999999995e-55"
     Typing          2751..4336
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atggtaaata cggagtattt taattgcggg cctttgttgt atatctctgt cgtttgtccc
       61 cggggggaag cattactgct aacaagtccc gtgagaaaac tgcgcaatcg tattgcgcac
      121 catgaaccta ttctcaaccg caatctggag gatgattttg ctacgataaa gagaattatc
      181 acgtatcggt gtcagcattc attggagtgg atgctgaaaa accaggtgtt actccctcta
      241 cttacactta aacctctcta aaaatataag taagtactat cgagggctat catgaactat
      301 ggtgccctct gagcatagct acccattact tcttctatgt cattgaataa ttcatttctt
      361 aactctaagt attctagtaa ctccatttct aatgactctg tcgtgaactt aaatctagaa
      421 ggatctttga ttgagtttac tagtcttgat aacgctctat atgttttgag tgaaggttgc
      481 attatagatg gaaagtattt gaaaacctct tcatctctgt tgaaattaac taaaaacttg
      541 tagtcatcat ttataaatct caagcataca gcgtcaagct tatcgccttt tcttattatt
      601 atttctttat aggaaagata tttttcagaa gataagtccc acatcaagcg aaaatctctc
      661 tttgcgaacg agttcgcgtc atcattgaaa agagatgatg tgatggcttt ggatagacct
      721 tctgtgttta tctctttgtt ggatgggtag taaattttat taattgcttt cattctctca
      781 aatgatgaat ataggtcatt atgccacctt gttgaaatca ctcctttagt tatattctcc
      841 ttgctaaaat taagccctgt atcaaaaata aatgcagcca tcagtgaata tgatatgttt
      901 tttattaact cagacttaaa tggttccgct atggagtagt acagtgataa aataactaaa
      961 aataaaaggt attgtcttac ctttcccgat gagtatatgt aaaggcgata tttatttatt
     1021 gatagtttta ttttgtatgg aatgatctca tttctgtcat atcctcttcg tggtggagca
     1081 aaacaaaaga aacatgcagc tattaataaa acaaaaaaga tgaacagtgt aagcaagttc
     1141 ggctcctgtg tatgctcact atgcatgatt gtcttgagat ctaacgatcc tgaaggtagt
     1201 cttgtccgta aacgaaaaaa ccgcccagca aggcggcttt tcgaaggttc tcagagcagc
     1261 aactctttga accaaggtaa ctggcttgga ggagcacagc caccaaatct gtcctttcag
     1321 tttagcctta accggcgcat aacttcaaga ctaactcctc taaacggtta ccaatggctg
     1381 ctgccagtgg cgtttttacg tgtctttccg ggttggactc aagacgatag ttaccggata
     1441 aggcgcagcg gtcgggctga acggggggtt cgtgcacaca gcccagcttg gagcgaacga
     1501 cctacaccgg gccgagatac caacagcgtg agctatgaga aagcgccacg cttcccgaag
     1561 ggagaaaggc ggacaggtat ccggtaagcg gcagggtcgg aacaggagag cgcacgaggg
     1621 agcttccagg gggaaacgcc tggtatcttt atagtcctgt cgggtttcgc cacctctgac
     1681 ttgagcatct gtttttgtga tgctcgtcag gggggcggag cctatggaaa aacgccagcg
     1741 gcgcggcctt cttcctgttc ctggcctttt gctcacatgt ttcttttggc gttatcccct
     1801 gattctgtgg ataaccgcat caccgtcttt gagtgagctg ataccgctcg ccgcagccga
     1861 acgaccgagc gtagcgagtc agtgagcgag gaagcggaag agcgcctgat gcggcatttt
     1921 ctccttacgc atctgtgcgg tatttcacac cgcatatggt gcacttttct tataatccgc
     1981 actgatgcca catagttaag ccagtataca ctccgctatc gctacgtgac tgggtcaggg
     2041 ctgcgccccg acacccgcta aaacccgctg acgcgccctg acgggcttgt ctgctcccgg
     2101 catccgctca caggcaagct gtgaacgtct ccgggagctg catgtttcag ttgctttcac
     2161 cgtcatcgcc gaagcgtgcg aggcaactac ggtagagttc gtcggcgtgg tcgtgaagtg
     2221 attcgcagat gtctgcctgt tcgtccgcgt ccagctcgtt gagtttttcc agcagggtca
     2281 gcgtctggct tctgataaag cgggccatgt taagggctgt tttttcctgt ttggtcatgg
     2341 tcttaaaagg gctgtttttt cctgtttggt catggtctta aggctcctta ataggggatt
     2401 ttttaggggg aatgataccg atgaaacgcg agaagatgct cacgatacgg gttagcgatg
     2461 aggagcacgc ccggttactg gaacgctgcg agggtaaacg actggcagaa tggatgcggc
     2521 gggtctgtct gggggagccg gttgcgcgca caggaaaact gccgacacta tcgccgccat
     2581 tgctgcggca tctggctgcc atcgggaaca atctgaacca gacagcccgg aaggtgaaca
     2641 gcggccactg gtcttcgatt gaccgggttc atgtggtggc cgctctgatg gccatcgagg
     2701 gtgaattgcg ccagttgcgg caggctgtca gggaacaggg ggggacggga tgatagttaa
     2761 atttcatgcc agggggaaag gcggtggaag tggcccggtc gattacctgc tggggcggga
     2821 gcgtaaccgc gaaggcgcaa cggtgctccg gggtaacccg gaagaaatcc gggaactcat
     2881 tgatgccacg ccattttcga agaaatacac gtcaggcgtt ctgtcgttcg cggagaagga
     2941 gttaccgccg ggtgaacgcg aaagagtgat gacgagcttt gagcgtgttc ttatgcccgg
     3001 tctcgaaaaa gaccagtaca gcattctctg ggtggaacac caggataagg ggcggctcga
     3061 actgaatttt gtcattccga acatggaact acagagcggt aagcgcctcc agccgtacta
     3121 cgaccgtgcg gacaggccga ggataaatgc ctggcagacg ctggttaatc atcattacgg
     3181 gctgcgtgac ccgaacgcac cggagaacag acggacgctt gtcacaccga ataatctgcc
     3241 aaaagcgaaa caggaggccg cagaagcgat tacacggggt cttgaggcgc tttaccgtgc
     3301 cggagcaata aaaacgcgtc aggatgtcac tgaggcgctc acagcggcag gttttgaggt
     3361 ggtgaggaca accagaagca gtatcagtat tgccgacccg gagggggggc ggaatctcag
     3421 gctaaagggg gcgctgtatg agcaatcttt tacaaatggg aacggacttc gagaagaaac
     3481 tgaaagagcg agccgcttct accgagaaca tgctgaacag cgagttcagg aagctagaag
     3541 agtctgtaga caaggcactg agcttaaaca ggcagaaaat cagagacgct atcagcgaac
     3601 atacaacatc cgtgaaacag caactggata cgctgagcac caccgtgagc acgcagctca
     3661 gcaccacaga ggccgaactg tcccggcagc agaaaaacct gctctggcag gtgatcaaag
     3721 ggcgggtact gtttccggcg ctgaccgcgc tcagcgtcac gggcggcatt ttcctggggt
     3781 gctgggggct gattcagtgg caggaaagca ggattgcgaa aaatatcttg accatcagag
     3841 agcaggaaaa cacgctggcg aaactcgagg caaaaacctg gggggtgacg ttcgtcaatg
     3901 gcgagaacgg gaaatttctg gtgctgccgg acggggtgaa aggggaaaac acctggacgg
     3961 tgggcgacaa gaacgccgtg aggctggtca gggagtaaac gagtatgacg gaactggaag
     4021 ggcatttgct gaacgcctta gagcatttgc aacaggacta tatgcggcgg ctgaacgagt
     4081 gggagagcgc cttcgcagaa ttgcagaaga tgcacgcggt tacgcaacag aacaacgcga
     4141 tactgaacga gcgtgtcgtg aacttgagtc agcaggtgca gctattagcc ggacaagtcg
     4201 accgcttgag tcggttattt atcacgaaca acagataagg gatgaacagg agcgtcaggc
     4261 gcaggagctt gcccggcgct ggcatgaaga gcaggaaccc gaagcgcgga tctggcgtgg
     4321 cccgtcaatg gggatgtgac cggggtaccc cctgaaatcg agccagtttg tggcacgccc
     4381 tacccggatg gcgccaatgt taatgtacgt acattagcat taacaatatc caaacctccc
     4441 cattttgccc cgttcgacgg ctggaacgtg cgaaactgat cgtcattcag tttcgcgcat
     4501 aactatgcat gaggttaaaa tttaccaggc gcgatcgcgg cagtttttcg ggtggtttgt
     4561 tgctgttttt acctgtctgc tgccgtgatc gcgctgaacg cgtttaagcg gtacgcgcaa
     4621 tgcgacgtt
//
