LOCUS       CP048872                5153 bp    DNA     circular BCT 22-DEC-2020
DEFINITION  Escherichia coli strain 6-Pyelo plasmid p6-Pyelo_2, complete
            sequence.
ACCESSION   CP048872
VERSION     CP048872.1
DBLINK      BioProject: PRJNA592372
            BioSample: SAMN13422981
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5153)
  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 5153)
  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                   :: 96x; 123x
            Sequencing Technology             :: Illumina MiSeq; PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 02/18/2020 18:24:22
            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)                     :: 5,096
            CDSs (total)                      :: 4,973
            Genes (coding)                    :: 4,828
            CDSs (with protein)               :: 4,828
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 95
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 145
            CDSs (without protein)            :: 145
            Pseudo Genes (ambiguous residues) :: 0 of 145
            Pseudo Genes (frameshifted)       :: 59 of 145
            Pseudo Genes (incomplete)         :: 76 of 145
            Pseudo Genes (internal stop)      :: 34 of 145
            Pseudo Genes (multiple problems)  :: 21 of 145
            ##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..5153
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="6-Pyelo"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p6-Pyelo_2"
                     /geo_loc_name="USA"
                     /collection_date="1995"
                     /collected_by="University of Minnesota, Minneapolis, MN"
     gene            join(5119..5153,1..307)
                     /locus_tag="G4281_25440"
     CDS             join(5119..5153,1..307)
                     /locus_tag="G4281_25440"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000058758.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin transporter"
                     /protein_id="QMX36612.1"
                     /translation="MSLRYYIKNILFGLYCALIYIYLITKNNEGYYFLASDKMLYAIVI
                     STILCPYSKYAIEHIFFKFIKKDFFRKRKNLNNAPVAKLNLFMLYNLLCLVLAIPFGLL
                     GLFISIKNN"
                     /name="colicin transporter"
     gene            complement(304..1869)
                     /locus_tag="G4281_25445"
     CDS             complement(304..1869)
                     /locus_tag="G4281_25445"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000447006.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin-10"
                     /protein_id="QMX36613.1"
                     /translation="METAVAYYKDGVPYDDKGQVIITLLNGNPDGSGSGGGGGTGGSKS
                     ESSAAIHATAKWSTAQLKKTQAEQAARAKAAAEAQAKAKANRDALTQHLKDIVNEALRH
                     NSTHPEVIDLAHANNAAMQAEAERLRLAKAEEKARKEAEAAEKAFQEAEQRRKEIEKEQ
                     AETERQLKLAEDEEKRLAALSEEARAVEVAQKNLAAAQSELAKVDEEINTLNTRLSSSI
                     HARDAETNTLSGKRNELDQASAKYKELDERVKLLSPRANDPLQSRPFFEATRLRARAGD
                     EMEEKQKQVTASETRLNQISSEINGIQEAISQANNKRSTAVSRIHDAEDNLKTAQTNLL
                     NSQIKDAVDATVSFYQTLSEKYGEKYSKMAQELADKSKGKKISNVNEALAAFEKYKDVL
                     NKKFSKADRDAIFNALEAVKYEDWAKHLDQFAKYLKITGHVSFGYDVVSDILKIKDTGD
                     WKPLFLTLEKKAVDAGVSYVVVLLFSVLAGTTLGIWGIAIVTGILCAFIDKNKLNTINE
                     VLGI"
                     /name="colicin-10"
     gene            2147..2566
                     /locus_tag="G4281_25450"
     CDS             2147..2566
                     /locus_tag="G4281_25450"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001711305.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="entry exclusion protein 1"
                     /protein_id="QMX36620.1"
                     /translation="MAWHTLRDALKMTGRSRSQFYRDMRSGLVSYRTSQDGRREFETSE
                     LIRAYGELKRNETPERHTQGHSEKPHDQQTERILRELNELKQCLTLMLEDKQAQDTERR
                     RQEAERKQLQNEIAQLRQALEQEKKRGFWSRLFGH"
                     /name="entry exclusion protein 1"
     gene            2647..3066
                     /gene="exc2"
                     /locus_tag="G4281_25455"
     CDS             2647..3066
                     /gene="exc2"
                     /locus_tag="G4281_25455"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016247941.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Exc2 family lipoprotein"
                     /protein_id="QMX36614.1"
                     /translation="MRRTGNKLCLIAMITATVALTACTPKGSVEQHTRHYVYASDDGFD
                     PNFSTQKADTTRMMVPFFRQFWDMGAKDKATGKSRSDVQQRIQQFHSQEFLNSLRGTTQ
                     FAGTDYRSKDLTPKKSRLLADTISAVYLDGYEGRQ"
                     /name="exc2"
     gene            complement(3291..3614)
                     /locus_tag="G4281_25460"
     CDS             complement(3291..3614)
                     /locus_tag="G4281_25460"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="nikA protein"
                     /protein_id="QMX36615.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="nikA protein"
     gene            3898..4092
                     /locus_tag="G4281_25465"
     CDS             3898..4092
                     /locus_tag="G4281_25465"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041639.1"
                     /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="QMX36616.1"
                     /translation="MNKQQQAVLNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA
                     EELQNSIQTRFEVENSTER"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            4280..4651
                     /locus_tag="G4281_25470"
     CDS             4280..4651
                     /locus_tag="G4281_25470"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003745291.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QMX36617.1"
                     /translation="MSKKQSTGRSQRRRRFSIGSAPLTSITKIDAQARGGETRQDYKDT
                     RRFPLEAPSCALLFRPCRLPDTCPPFSLREAWRFLIAHAVGISARCRSFAPSWAVCTNP
                     PFSPTAAPYPVTIVLSPTR"
                     /name="hypothetical protein"
     gene            4579..4737
                     /locus_tag="G4281_25475"
     CDS             4579..4737
                     /locus_tag="G4281_25475"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354639.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="QMX36618.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLAPLAAAVGNLVSRAMMA
                     QMVQQSS"
                     /name="replication initiation protein"
     gene            complement(4934..5071)
                     /locus_tag="G4281_25480"
     CDS             complement(4934..5071)
                     /locus_tag="G4281_25480"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001329514.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin E1 lysis protein"
                     /protein_id="QMX36619.1"
                     /translation="MRKRFFVGIFAINLLVGCQANYIRDVQGGTVAPSSSSKLTGISVQ
                     "
                     /name="colicin E1 lysis protein"
     Typing          complement(3624..3863)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="7.6e-123"
     Typing          4122..4651
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.59"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          complement(3295..3614)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="3.11e-62"
ORIGIN
        1 tggcctatac tgcgcactta tatatatata ccttataaca aaaaacaacg aagggtatta
       61 tttcctagcg tcagataaga tgctatacgc aatagtgata agcactattc tatgcccata
      121 ttcaaaatat gctattgaac acatattttt taagttcata aagaaagatt ttttcagaaa
      181 aagaaaaaac ctaaataatg cccccgtggc aaaattaaac ctatttatgc tatacaatct
      241 actttgtttg gtcctagcaa tcccatttgg attgctagga ctgtttatat caataaagaa
      301 taattaaata cccaacacct catttatagt attaagttta ttcttatcaa taaaggcaca
      361 tagaatgcct gtaacaatag caatccccca gatacctaat gtagttccag caagcacact
      421 aaaaagtaaa acaacaacat aactaactcc agcatctaca gctttcttct ctaatgtaag
      481 aaatagcggc ttccagtcac ctgtatcctt aatttttagg atatcagata ccacatcata
      541 tccaaaagaa acatgtcccg taatcttcaa gtacttggca aactgatcta aatgcttagc
      601 ccagtcttca tacttaaccg cctccagtgc attgaaaatt gcatcacggt ctgctttgct
      661 gaatttctta tttaatacat ccttgtattt ctcaaaagca gctagagctt cattcacatt
      721 gctgattttc ttacctttag atttatcagc aagttcctgt gccatttttg aatatttttc
      781 accatatttt tcagatagcg tttgataaaa gctaactgtt gcatccacag catccttaat
      841 ctgcgagttc aggagattag tctgtgctgt tttcaaatta tcttcagcat catgaatacg
      901 tgaaactgct gtacttcgct tattattagc ctgagaaata gcctcttgga ttccatttat
      961 ctcagagcta atctggttaa gacgcgtttc tgatgctgtt acctgctttt gtttttcctc
     1021 catctcatca ccagctctcg cccgtagtct ggtggcctca aaaaaaggac gactctgaag
     1081 cggatcattc gccctaggag ataaaagttt aaccctttca tccagttctt tatatttagc
     1141 agatgcctga tccaactcat ttcgttttcc ggacagcgta ttcgtttctg catcacgggc
     1201 atgaatactg gagcttaaac gggtattgag cgtattaatc tcttcatcca ctttcgccag
     1261 ctcagattgt gcagcagcaa gatttttttg tgccacctcc acagcccggg cctcttcact
     1321 caatgctgcc aggcgtttct cttcatcctc agccagtttc aattggcgtt ctgtttcagc
     1381 ctgctccttc tctatctctt tacgtcgttg ttctgcttcc tgaaaagcct tttccgcagc
     1441 ttccgcttct ttacgggctt tttcttctgc ttttgcaagg cgcaaccgct ctgcttctgc
     1501 ctgcatcgct gcattattgg catgagccag gtcaataacc tccggatgag tggaattatg
     1561 gcgaagcgcc tcattcacaa tatccttcag atgttgagtc agcgcatccc ggtttgcttt
     1621 tgctttagcc tgtgcttctg cggcagcttt tgctcgggca gcctgttctg cctgcgtttt
     1681 cttcaattga gcagtagacc atttagctgt ggcatgaatg gctgcagaac tttcactttt
     1741 gctacctcca gttccaccac caccgccaga gccactcccg tctggattac cattcaaaag
     1801 agtaatgatt acctgcccct tatcatcata aggaacacca tctttatagt acgctacagc
     1861 tgtttccatt ataaaatcct ctttgacatt aaaaacaaat agttaaaagc aatatactgt
     1921 atatataatc actggtttta tatacagttt aaaattacgc cgctgcattt tccctgtcaa
     1981 ccctgtggat tttcattttt gtgaaaacga tcaaaaaaac agccacccac accacgtgct
     2041 atttccaccc gatgccacaa aaaccagcac aaacattacc gttctcagac ctcattatgt
     2101 tttactgaaa ccatgagatg agacacctat gggacactgt aactttatgg catggcacac
     2161 actccgggac gcactgaaaa tgactggaag atcgcgttca cagttttacc gtgatatgcg
     2221 ctcaggtctt gtcagttacc gtaccagcca ggacggacga cgggagtttg aaaccagtga
     2281 actgatccgg gcatacggcg aattaaagcg gaatgagaca ccagaaaggc acactcaagg
     2341 acactcagaa aaacctcatg atcagcagac agaacgcatt ctccgggaac tgaatgagct
     2401 gaaacaatgc ctgacgctga tgcttgagga taaacaagcc caggatacgg agcgccggcg
     2461 ccaggaagca gaacggaaac agctacagaa tgagatagcc cagctcaggc aggctctgga
     2521 gcaggaaaag aaacggggat tctggtccag gctgttcggt cactgaacgc gctcagaaac
     2581 tgatgataag ataatcttcg gataataact caccgagaat aaatacttta aggtagggag
     2641 acactcatga gacgtaccgg aaacaaactt tgtcttatcg ccatgataac agcaacagta
     2701 gctctcacag cctgtacccc aaagggcagc gtggaacaac atacccggca ttacgtatat
     2761 gcttctgatg acggttttga tcccaacttt tccacccaaa aagccgacac aacacgaatg
     2821 atggtgcctt tttttcggca gttctgggat atgggagcta aagataaagc gacaggaaaa
     2881 tcacggagtg atgtgcaaca acgcattcaa cagtttcaca gccaggaatt tttaaactca
     2941 ctccggggca caactcaatt tgcgggtact gattaccgca gcaaagacct taccccgaaa
     3001 aaatccaggc tgctggctga cacgatttct gcggtttatc tcgatggcta cgagggcaga
     3061 cagtaagtgg atttaccata atcccttaat tgtacgcacc actgaaacgc gctgaacgcg
     3121 attctgacgc agacaccgca aaaagagatg ttttaccccg gaaaaacagg aaggatgcgt
     3181 caggatcgtt ttcagctctc tgcatagcta tgcatgaaag cgaatggtga tcactttggg
     3241 agcttacggt gttcataccg tcagttttcg acagttttct ctccgggaag ctaatctgcc
     3301 ataagcctgg ataacagggc acggtgatac tccgtaatag cgatcagcac ctccgcatac
     3361 tccctgtccc cgacacgctt gccgtcgata aagagttttt tctgtaacgc ccccagtctc
     3421 ataacttctt tcagtacccg atcatcagtc agtgagttaa ctttcttacc gagagctgcc
     3481 gcccgtaaaa aaccggaaac ggtcttgccg cattcagcag ccctttttct gatttcctgg
     3541 tcttcttctg ccgtcagacg aacagggcga ctgatagccc gcctgcgcgt attacttcca
     3601 cttcgttttg tcataaaaca tggctccgta tctgacatgg gtgtcggggc aaagccctga
     3661 ccagggtaat tgtaatagcg tgcatgtatg cgcggtataa caattacaca tcctgtcctg
     3721 tcagcaagtt cgaattaccg acaaaggcac ggcagttttt tggcagtgac agtattgtca
     3781 ggcagaaata cccgtcaaag cgtcagacgg cagaataccg gcggtaaaac agtcgaaaag
     3841 tggtacgcga tataatcaca caacgcagat gacagacaga acggagaaaa cgaaaagatg
     3901 aacaagcagc agcaagccgt actcaacatg gcaggattca taaaaagcca aagcctgacg
     3961 ctgctcgaaa agctggacgc actcgatgct gacgaacagg ctaccatgtg tgagaagctg
     4021 cacgaactcg cagaagaact ccagaacagc atccagacac gctttgaagt agaaaatagc
     4081 acagagagat aacgctcagg acaggatgcc gaacggcaca acagagcgta aggagaaaat
     4141 gtcacataag gcgctcttcc gcttcctcgc tcactgactc gctacgctcg gacgttcgac
     4201 tgcggcgagc ggtgtcagct cactcaaaag cggtaatacg gttatccaca gaatcagggg
     4261 ataaagccgg aaagaacatg tgagcaaaaa gcaaagcacc ggaagaagcc agcgccgcag
     4321 gcgtttttcc ataggctccg cccccctgac gagcatcaca aaaatcgacg ctcaagccag
     4381 aggtggcgaa acccgacagg actataaaga taccaggcgt ttccccctgg aagctccctc
     4441 gtgcgctctc ctgttccgac cctgccgctt accggatacc tgtccgcctt tctcccttcg
     4501 ggaagcgtgg cgctttctca tagctcacgc tgttggtatc tcggctcggt gtaggtcgtt
     4561 cgctccaagc tgggctgtgt gcacgaaccc cccgttcagc ccgaccgctg cgccttatcc
     4621 ggtaactatc gtcttgagtc caacccggta agacacgact tagcgccact ggcagcagcc
     4681 gttggtaact tggttagcag agcgatgatg gcgcaaatgg tgcaacagag ttcttgaagt
     4741 agtggcccga ctacggctac actggaagga cagtatttgg tatctgcgct ctgctgaagc
     4801 cagttacctc ggttaagcag ttccccaact gacttaacct tcgatcaaac cgcctcccca
     4861 ggcggttttt tcgtttacag gcagcagatt acgcgcagaa aaaaaggatc tcaagaagat
     4921 cctttgatct tttctactga acagagatcc ccgtcaattt agaagaagat gatggagcca
     4981 cagtccctcc ctgaacatca cgtatatagt tagcctgaca tccaacaagg aggtttatag
     5041 cgaatattcc cacaaaaaat cttttcctca taactcgatc cttataaaat gaaaagaata
     5101 tataacgagg tttaatttat gagtttaaga tactacataa aaaatatttt gtt
//
