LOCUS       NZ_CP076696             5168 bp    DNA     circular CON 18-JUL-2023
DEFINITION  Escherichia coli strain S103EC plasmid pS103EC_B, complete sequence.
ACCESSION   NZ_CP076696
VERSION     NZ_CP076696.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN19700014
            Assembly: GCF_018972265.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5168)
  AUTHORS   Alvarez-Fraga,L., Phan,M.D., Goh,K.G.K., Nguyen,T.K.N.,
            Hancock,S.J., Allsopp,L.P., Peters,K.M., Forde,B.M., Roberts,L.W.,
            Totsika,M., Beatson,S.A., Ulett,G.C. and Schembri,M.A.
  TITLE     Differential Afa/Dr fimbriae expression in the multidrug resistant
            Escherichia coli ST131 clone
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5168)
  AUTHORS   Alvarez-Fraga,L., Phan,M.D., Goh,K.G.K., Nguyen,T.K.N.,
            Hancock,S.J., Allsopp,L.P., Peters,K.M., Forde,B.M., Roberts,L.W.,
            Totsika,M., Beatson,S.A., Ulett,G.C. and Schembri,M.A.
  TITLE     Direct Submission
  JOURNAL   Submitted (14-JUN-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                     :: JUN-2021
            Assembly Method                   :: flye v. 2.5
            Assembly Name                     :: S103EC
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 149x
            Sequencing Technology             :: Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/18/2023 04:24:40
            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)                     :: 5,293
            CDSs (total)                      :: 5,176
            Genes (coding)                    :: 4,954
            CDSs (with protein)               :: 4,954
            Genes (RNA)                       :: 117
            rRNAs                             :: 9, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 222
            CDSs (without protein)            :: 222
            Pseudo Genes (ambiguous residues) :: 0 of 222
            Pseudo Genes (frameshifted)       :: 83 of 222
            Pseudo Genes (incomplete)         :: 162 of 222
            Pseudo Genes (internal stop)      :: 41 of 222
            Pseudo Genes (multiple problems)  :: 56 of 222
            Pseudo Genes (short protein)      :: 3 of 222
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP076696.1.
            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..5168
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="S103EC"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pS103EC_B"
                     /geo_loc_name="Australia:Brisbane"
                     /collection_date="2010-01"
     gene            1..915
                     /locus_tag="KQ261_RS26230"
                     /old_locus_tag="KQ261_26230"
     CDS             1..915
                     /locus_tag="KQ261_RS26230"
                     /old_locus_tag="KQ261_26230"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001738986.1"
                     /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_001271348.1"
                     /translation="MSAALQYFDENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWLVMEWREEAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLEAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGSKSKRSTVATSARTL
                     KPWEALGISRAWYYQLKKRGLVE"
                     /name="replication initiation protein"
     gene            complement(1119..1517)
                     /locus_tag="KQ261_RS26235"
                     /old_locus_tag="KQ261_26235"
     CDS             complement(1119..1517)
                     /locus_tag="KQ261_RS26235"
                     /old_locus_tag="KQ261_26235"
                     /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="hypothetical protein"
                     /protein_id="WP_001222914.1"
                     /translation="MRISNIEWLKKRIGFIRKLGEQTARQRQIIDLIDNEAGLTEQERK
                     LLHVLATAEKNDLQAQESERKQAVQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELCYKKDRILQALKELKYDLETSPNPDA"
                     /name="hypothetical protein"
     gene            1694..2620
                     /locus_tag="KQ261_RS26240"
                     /old_locus_tag="KQ261_26240"
     CDS             1694..2620
                     /locus_tag="KQ261_RS26240"
                     /old_locus_tag="KQ261_26240"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221102.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_001331297.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTPEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIDGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     LTQQKEQLRELRKRWEVKHNEHMRKHGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIREWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQNRTAPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            2623..3157
                     /locus_tag="KQ261_RS26245"
                     /old_locus_tag="KQ261_26245"
                     /pseudo=""
     CDS             2623..3157
                     /locus_tag="KQ261_RS26245"
                     /old_locus_tag="KQ261_26245"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221103.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     gene            complement(3223..3432)
                     /locus_tag="KQ261_RS26250"
                     /old_locus_tag="KQ261_26250"
     CDS             complement(3223..3432)
                     /locus_tag="KQ261_RS26250"
                     /old_locus_tag="KQ261_26250"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001618649.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001096196.1"
                     /translation="MAKLGENTPHIIDATVDFMASSQAFREYLKKLPPDNTIPPALTDE
                     HVPLYIRRLEYYRLLYRPKQTESY"
                     /name="hypothetical protein"
     gene            complement(4581..4889)
                     /locus_tag="KQ261_RS26255"
                     /old_locus_tag="KQ261_26255"
     CDS             complement(4581..4889)
                     /locus_tag="KQ261_RS26255"
                     /old_locus_tag="KQ261_26255"
                     /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="hypothetical protein"
                     /protein_id="WP_023909142.1"
                     /translation="MALHNYARKRCAIGFVRSEHRTAQNDKFSPLVRGALTGFPVSKLH
                     ISPGQKKTDLGSVARIRVYGKYFSYRMLNIHKRKKCLSDALKQPFQKESALYDARKR"
                     /name="hypothetical protein"
     Typing          2..776
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.778"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          1695..2617
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.052"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgagcgccg cgcttcaata cttcgacgaa aatttacccc atcgtcccta tcacacggat
       61 gatctcgctt ttggtcttcg catctccggc aaagggcgtg cgcttcttgc gcggtacata
      121 cagcagaacc agcctcatgc gcagttctgg ctggtttttg acgttgaccg cgagggggct
      181 gcgattgact ggagcgaccg gaacgctccc gcgccgaaca tcaccgttaa aaatcctgtg
      241 aacggacacg ctcacctgct ctacgcactc aacatcgccg tgagaaccgc gcctgatgcc
      301 tcggttaagg cgctgaaata tgccgcagcg gttgaacgtt cgctgtgtga gaaactttgt
      361 gcggatgtga actacagcgg cctgatttgc aaaaatccgt tccacctgga atggctggtg
      421 atggagtggc gcgaggaagc ctataccctc gatgaactgg ctgattatct cgatttgagc
      481 gcctcagagc gtcgtagcat cgataaacat tacgggatgg ggcgaaactg ccacctgttc
      541 gaaatgacgc gcaaatgggc ttacagggcg attcgtcagg gctggccagc gttctcacag
      601 tggcttgaag cggtgatcca gcgtgtcgaa atgtacaatg catcgcttcc cgttccgctt
      661 tcactggctg aatgtcgggc tattggcaag agcattgcga aatacacgca caggaacttc
      721 acgccggaaa ctttcgcaca gtatgtggct gatacgcaca cgccagaaat tcaggctgca
      781 cgcggtcgca agggcggttc taagtctaag cgcagcacag tagctacatc tgcacgcacg
      841 ctgaaaccgt gggaggcatt agggatcagt cgcgcctggt attaccaact gaaaaaacga
      901 ggtctcgtag agtagaccaa ataagcctat atcagataac agcgcctttc tggcgtcttt
      961 ttgagcagca ggttttttgc cgtttttccc cgttcagccc tgcaatggcg cggctttccg
     1021 cgtgattgtg gtggtagtgc tcgccgcagt ctcatgaccg agcgtagcga gcgaatgagc
     1081 gaggaagcac cagggaatcg gaacacggat ggaggcactt acgcgtctgg gtttggggat
     1141 gtctccagat cgtacttaag ttccttaagt gcttgtaata tcctgtcttt tttatagcat
     1201 agctcgcctg tttttgtgtc taccagtcct gcttcgatca gtagcccagc cgcgagaaag
     1261 agccggtgat tgcgttcccg tcgttgtttt tttccctcga ttcgtttttg gaccgcctgt
     1321 tttcgttcgc tctcctgtgc ctgtaagtcg tttttttccg ctgttgccag tacgtggaga
     1381 agtttgcgtt cctgttctgt gagtccggct tcgttgtcga tcaggtcaat aatctgtctc
     1441 tgtcgtgcgg tctgttctcc gagcttcctg atgaatccga tccgtttctt cagccattcg
     1501 atgttgctga tgcgcatgtt cgtgatgctc cctggtgttt ttttgcggtg tgttgtggtc
     1561 gtgcagtata tcgcttgcgg tcggcgggtg cagggggtat cttccgtgct aattcgtaaa
     1621 attagaagga agcgcactta tatgtttctc tccttcgtcg agaaacagtg cgctcctgca
     1681 gagggctgaa accgtggcaa cctatcacct cagcgttaaa tttggtggca aggggcaggc
     1741 tgcaaaccac gccgattaca tcgagcgcaa agagaaatac cgcgaccgtc aggatttgga
     1801 atattccgca cacggaaaca tgccggaatg ggccagggat aatccttccc atttctggca
     1861 ggcggctgac cagtttgaac gtgcgaacgg ttcgacctat agggaacttg aaattgcatt
     1921 accccgtgaa ctgacaccgg aacagcgcct tgaactggtg caggattttg tacgtcagga
     1981 agctggcgaa cggcacgcct ggagttttgc cattcacaat ccgaaagcga gcattgacgg
     2041 cggcgaacag cctcatgcgc atatcatgat gagtcagcgt gtgaatgatg gcattgaacg
     2101 tacaccggaa cagtatttcc ggcgctataa cgccaggtat cccgagcggg gaggtgcgaa
     2161 aaaggattcc ggaagcctga ctctcactca gcaaaaagag cagttgcggg aattgcgaaa
     2221 acgctgggag gtgaagcaca acgaacatat gagaaagcat ggctttgaaa ggggcttcat
     2281 tgactgccgg acgctgaaag aacagggcat tgaacgacgt cccgaagtgc atctgggttt
     2341 tgaagctgcc ggacggcttg atgatgccca gcgtcatgac atcatgcaaa aacggtctga
     2401 accggactat tcccgccatc ttgaacaggc gcgaacggtc gggcatgaca tcagggaatg
     2461 gctggacact ccggttaagc aacatgaact ggtcagaagg ctgcaacatg atgttgcgcg
     2521 ggagcatggc tttgacatga gagacagagt gagcagacag aaccgaactg cacctgaacg
     2581 ggttaaatca ccgtcacgtg gattttctat gggattctga acatggccag cacagaagaa
     2641 aaattactca cgctcctgtt atcggtggag catctgcaac ataccgcaat ggagcaacag
     2701 aaagctgttg ctgattctct ggctgtggca agggaaactc ttcgcggata tcgggatatt
     2761 tctgacgggt gtggcaaaac aggtcaggga tgaagtcaga aatgaggtgc agaagctgga
     2821 cgtggcagga ctgataggtg agcgcatcag ccaggatttt cagcggctgg aagagtcagt
     2881 cgcaaacatg aaggcaaacg cggatgccct gaacagggat attgcgacaa ttcacagcaa
     2941 tatcgtgcag gaatacaaca cccttaaagg gtatagctgg aaatggctgg gtggggtgtc
     3001 agtggctttt ctggttatgt tctgtgtgct cggatgggga atgaaaacaa tactcgacag
     3061 gaactacaac gccacagcgg cggtgtatca gaaagttgtg acactggaag ataaactggt
     3121 ggagaaacct gtcacgggga agagccggaa aaactgacgc gcttcgcttg tccaacgcct
     3181 cacgacccgc gaaaggattt cgcgaaccgt tcaccgtttt tttcaatatg attctgtctg
     3241 ctttggtcga taaagcagac gatagtattc cagccttcgt atatataacg gtacgtgctc
     3301 atcagtaaga gctggcggta ttgtgttatc agggggaagt tttttcagat actcacgaaa
     3361 tgcctggctt gatgccataa aatctacagt agcatcgata atatgtgggg tgttttcacc
     3421 taattttgcc atgatgataa tccttatatt atcacggttt gtgaatgata gggtgtcact
     3481 attatttatg cgttagtgaa ccagaaaaaa tcccccgttg gcataggggg atatgtaagg
     3541 agaaataact tcgcaggtgt tcttgtttgt ataacgtgaa aagactgcac gcaacttaat
     3601 aagtctgccg tacttacttt cagttttcaa cataaggttt ataacaatgt atggaatgga
     3661 agtgagcttt aaggtttcag ctctaaaaaa taaaatattt attagttggc tggttgttgt
     3721 tcttgttctg tatgtatata aacactatcg acatattatg accgggaaca ttccttaccc
     3781 cctctgcgct cgcagaggtt ttttttgtca ttaattaata atgaactgaa atgcagttcc
     3841 gatacctcca tttgcacatt atccctgaca tatggtaccg gaaccgcatt aattttatgt
     3901 tataagagtt tatttttaat gtccagatgg tttaatagta tttatatgta attagctgta
     3961 tggatagtac tggttttatt gtataacttg tcgttttttt ttattgtttt tgtgtggtgt
     4021 gctaatcttt aagttataaa aaaacccctt ggaatacagg ggcaaaagta aggaaaacaa
     4081 atggatgctc agtttgtgtg acactttaaa ctaatggaac tatagagtgg aggttgttac
     4141 agtcgctttt ataaaacagc aaccagtttt tttcaatagt ctgatgatgg ttgtgacagt
     4201 tttgtgatat tgttcaaaat gtttcttgtt gaatgtttgt tttttggtct attggtgtct
     4261 ggttttattt tttctgctat tacatatcaa gaaatgtgat tggtgtagca agagtggaat
     4321 gcgatgtgga taaactaatt ggttgtcgaa tctaatttac ttagaaaact acacttgttt
     4381 ttgtgtatga atttagtgaa tttgtctgtc tatgtgtttt cgtgcattta taaatccttc
     4441 gtcaggatct taaatttagt gttgaatatg tagggcctgt acggtaatta ttatttagcg
     4501 tagctacttc atcgttgttc gaacacaacc aacaacctgt aattgttgtt tctcttggtt
     4561 ccccactttt gtggggtttt ttatctcttc cgtgcatcgt aaagcgcgga ctccttctgg
     4621 aaaggttgtt ttagggcatc actgaggcat tttttgcgtt tgtgaatatt gagcatccga
     4681 taactaaaat atttcccata gactctgatt cttgccaccg accccaggtc ggtttttttt
     4741 tgtcctggcg agatgtgaag tttggaaaca ggaaaccccg tcagagcgcc acgcaccagg
     4801 ggagaaaact tgtcgttttg agccgttcgg tgttcagaac gcacgaaacc gatcgcacat
     4861 cgctttcgtg catagttatg caacgccatg aaaacgattc tgacgcgttt ttctggtttg
     4921 gcctggtgtt ttcttgtctt tttgcgtttt ttgcgccaga aagcgactga gggcgtttta
     4981 aggggggcgt acaacgggag ttatggtaaa tggatcgggt tttcgggaag gttcgacagg
     5041 atttgccgtt gggtgtagtg taagcgactg aaaaacaaac gcccctgaaa tcatgtccag
     5101 atccggcaag attcaacatg aaatacagag ggcgtgtagg tcgcataacc cggagagaat
     5161 cgtaacac
//
