LOCUS       CP048874                5163 bp    DNA     circular BCT 22-DEC-2020
DEFINITION  Escherichia coli strain 2-Pyelo plasmid p2-Pyelo_1, complete
            sequence.
ACCESSION   CP048874
VERSION     CP048874.1
DBLINK      BioProject: PRJNA592372
            BioSample: SAMN13422969
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5163)
  AUTHORS   Biggel,M., Xavier,B.B., Johnson,J.R., Nielsen,K.L.,
            Frimodt-Moller,N., Matheeussen,V., Goossens,H., Moons,P. and Van
            Puyvelde,S.
  TITLE     Horizontally acquired papGII-containing pathogenicity islands
            underlie the emergence of invasive uropathogenic Escherichia coli
            lineages
  JOURNAL   Nat Commun 11 (1), 5968 (2020)
   PUBMED   33235212
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 5163)
  AUTHORS   Biggel,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (14-FEB-2020) Vaccine & Infectious Disease Institute, LMM,
            University of Antwerp, Universiteitsplein 1, Antwerpen 2610, Belgium
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2019
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 68x; 228x
            Sequencing Technology             :: Illumina MiSeq; PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 02/18/2020 18:04:54
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 4.11
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 4,858
            CDSs (total)                      :: 4,733
            Genes (coding)                    :: 4,651
            CDSs (with protein)               :: 4,651
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 82
            CDSs (without protein)            :: 82
            Pseudo Genes (ambiguous residues) :: 0 of 82
            Pseudo Genes (frameshifted)       :: 37 of 82
            Pseudo Genes (incomplete)         :: 44 of 82
            Pseudo Genes (internal stop)      :: 15 of 82
            Pseudo Genes (multiple problems)  :: 12 of 82
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            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/
FEATURES             Location/Qualifiers
     source          1..5163
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="2-Pyelo"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p2-Pyelo_1"
                     /geo_loc_name="USA"
                     /collection_date="1995"
                     /collected_by="University of Minnesota, Minneapolis, MN"
     gene            1..915
                     /locus_tag="G4282_24270"
     CDS             1..915
                     /locus_tag="G4282_24270"
                     /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="plasmid replication protein"
                     /protein_id="QMX41267.1"
                     /translation="MSAALQYFEENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWLVMEWREEAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLEAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGSKSKRSTVATSARTL
                     KPWEALGISRAWYYQLKKRGLVE"
                     /name="plasmid replication protein"
     gene            complement(1119..1637)
                     /locus_tag="G4282_24275"
     CDS             complement(1119..1637)
                     /locus_tag="G4282_24275"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221101.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QMX41268.1"
                     /translation="MRFLLILRISTEDTPCTRRPQAIYCTTTTHRKKTPGSITNMRISN
                     IEWLKKRIGFIRKLGEQTARQRQIIDLIDNEAGLTEQERKLLHVLATAEKNDLQAQESE
                     RKQAVQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTGELCYKKDRILQALKELKYD
                     LETSPNPDA"
                     /name="hypothetical protein"
     gene            1694..2620
                     /locus_tag="G4282_24280"
     CDS             1694..2620
                     /locus_tag="G4282_24280"
                     /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="QMX41269.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTPEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIDGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     LTQQKEQLRELRKRWEVKHNEHMRKHGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIREWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQNRTAPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            2623..3156
                     /locus_tag="G4282_24285"
     CDS             2623..3156
                     /locus_tag="G4282_24285"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221103.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QMX41270.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQKLDVAGLIGERISQDFQRLEESVANMKANADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFCVLGWGMKTILDRNYNATAAVYQKVVTLED
                     KLVEKPVTGKSRKN"
                     /name="hypothetical protein"
     gene            complement(3222..3431)
                     /locus_tag="G4282_24290"
     CDS             complement(3222..3431)
                     /locus_tag="G4282_24290"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_019842149.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QMX41271.1"
                     /translation="MAKLGENTPHIIDATVDFMASSQAFREYLKKLPPDNTIPPALTDE
                     HVPLYIRRLEYYRLLYRPKQTESY"
                     /name="hypothetical protein"
     Typing          2..915
                     /name="rep_cluster_2131"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.909"
                     /coverage="100.0"
                     /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 cttcgaagaa aatttacccc accgtcccta tcacacggat
       61 gatctcgctt tcggccttcg tatctccggc aaagggcgcg cgcttcttgc acggtatatc
      121 cagcagaacc agcctcatgc acagttctgg 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 tctgacggtg tggcaaaaca ggtcagggat gaagtcagaa atgaggtgca gaagctggac
     2821 gtggcaggac tgataggtga gcgcatcagc caggattttc agcggctgga agagtcagtc
     2881 gcaaacatga aggcaaacgc ggatgccctg aacagggata ttgcgacaat tcacagcaat
     2941 atcgtgcagg aatacaacac ccttaaaggg tatagctgga aatggctggg tggggtgtca
     3001 gtggcttttc tggttatgtt ctgtgtgctc ggatggggaa tgaaaacaat actcgacagg
     3061 aactacaacg ccacagcggc ggtgtatcag aaagttgtga cactggaaga taaactggtg
     3121 gagaaacctg tcacggggaa gagccggaaa aactgacgcg cttcgcttgt ccaacgcctc
     3181 acgacccgcg aaaggatttc gcgaaccgtt caccgttttt ttcaatatga ttctgtctgc
     3241 tttggtcgat aaagcagacg atagtattcc agccttcgta tatataacgg tacgtgctca
     3301 tcagtaagag ctggcggtat tgtgttatca gggggaagtt ttttcagata ctcacgaaat
     3361 gcctggcttg atgccataaa atctacagta gcatcgataa tatgtggggt gttttcacct
     3421 aattttgcca tgatgataat ccttatatta tcacggtttg tgaatgatag ggtgtcacta
     3481 ttatttatgc gttagtgaac cagaaaaaat cccccgttgg cataggggga tatgtaagga
     3541 gaaataactt cgcaggtgtt cttgtttgta taacgtgaaa agactgcacg caacttaata
     3601 agtctgccgt acttactttc agttttcaac ataaggttta taacaatgta tggaatggaa
     3661 gtgagcttta aggtttcagc tctaaaaaat aaaatattta ttagttggct ggttgttgtt
     3721 cttgttctgt atgtatataa acactatcga catattatga ccgagaacat tccttacccc
     3781 ctctgcgctc gcagaggttt tttttgtcat taattaataa tgaactgaaa tgcagttccg
     3841 atacctccat ttgcacatta tccctgacat atggtaccgg aaccgcatta attttatgtt
     3901 ataagagttt atttttaatg tccagatggt ttaatagtat ttatatgtaa ttagctgtat
     3961 ggatagtact ggttttattg tataacttgt cgtttttttt attgtttttg tgtggtgtgc
     4021 taatctttaa gttataaaaa accccttgga atacaggggc aaaagtaagg aaaacaaatg
     4081 gatgctcagt ttgtgtgaca ctttaaacta atggaactat agagtggagg ttgttacagt
     4141 cgcttttata aaacagcaac cagttttttt caatagtctg atgatggttg tgacagtttt
     4201 gtgatattgt tcaaaatgtt tcttgttgaa tgtttgtttt ttggtctatt ggtgtctggt
     4261 tttatttttt ctgctattac atatcaagaa atgtgattgg tgtagcaaga gtggaatgcg
     4321 atgtggataa actaattggt tgtcgaatct aatttactta gaaaactaca cttgtttttg
     4381 tgtatgaatt tagtgaattt gtctgtctat gtgttttcgt gcatttataa atccttcgtc
     4441 aggatcttaa atttagtgtt gaatatgtag ggcctgtacg gtaattatta tttagcgtag
     4501 ctacttcatc gttgttcgaa cacaaccaac aacctgtaat tgttgtttct cttggttccc
     4561 cacttttgtg gggtttttta tctcttccgt gcatcgtaaa gcgcggactc cttctggaaa
     4621 ggttgtttta gggcatcact gaggcatttt ttgcgtttgt gaatattgag catccgataa
     4681 ctaaaatatt tcccatagac tctgattctt gccaccgacc ccaggtcggt ttttttttgt
     4741 cctggcgaga tgtgaagttt ggaaacagga aaccccgtca gagcgccacg caccagggga
     4801 gaaaacttgt cgttttgagc cgttcggtgt tcagaacgca cgaaaccgat cgcacatcgc
     4861 tttcgtgcat agttatgcaa cgccctgaaa acgattctga cgcgtttttc tggtttggcc
     4921 tggtgttttc ttgtcttttt gcgttttttg cgccagaaag cgattgaggg cgttttacat
     4981 ggtacgtaca acgggagtta tggtaaatgg atcggatttg cgggaaggct cgacaggttt
     5041 tgtcgttggg ggtagtgtaa gcgactgaaa aacaaacgcc cctgaaattc gtgtctatcc
     5101 gccaagactt tcacgaaaat acaggggcga tgtcggtcga taacctggaa ggaatcgtaa
     5161 cac
//
