LOCUS       NZ_CP035480             5209 bp    DNA     circular CON 18-JUN-2024
DEFINITION  Escherichia coli strain U13A plasmid pU13A_C, complete sequence.
ACCESSION   NZ_CP035480
VERSION     NZ_CP035480.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10817700
            Assembly: GCF_004135165.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5209)
  AUTHORS   Forde,B.M., Roberts,L.W., Phan,M.-D., Peters,K.M., Fleming,B.A.,
            Russell,C.W., Lenherr,S.M., Myers,J.B., Barker,A.P., Fisher,M.A.,
            Chong,T.-M., Yin,W.-F., Chan,K.-G., Schembri,M.A., Mulvey,M.A. and
            Beatson,S.A.
  TITLE     Personalised genomic investigation reveals strain heterogeneity
            during chronic infection with E. coli ST131
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5209)
  AUTHORS   Forde,B.M.
  TITLE     Direct Submission
  JOURNAL   Submitted (24-JAN-2019) School of Chemistry and Molecular
            Biosciences, The University of Queensland, Building 76, Cooper Road,
            St Lucia, QLD 4072, Australia
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2017
            Assembly Method                   :: HGAP v. 2.3.0
            Assembly Name                     :: UTAH_U13A_1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 120.0x
            Sequencing Technology             :: PacBio RSII; Illumina NextSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_004135165.1-RS_2024_06_18
            Annotation Date                   :: 06/18/2024 04:39:49
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,276
            CDSs (total)                      :: 5,163
            Genes (coding)                    :: 4,925
            CDSs (with protein)               :: 4,925
            Genes (RNA)                       :: 113
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 238
            CDSs (without protein)            :: 238
            Pseudo Genes (ambiguous residues) :: 0 of 238
            Pseudo Genes (frameshifted)       :: 91 of 238
            Pseudo Genes (incomplete)         :: 176 of 238
            Pseudo Genes (internal stop)      :: 41 of 238
            Pseudo Genes (multiple problems)  :: 60 of 238
            Pseudo Genes (short protein)      :: 1 of 238
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP035480.1.
            Bacteria and source DNA available from Schembri lab, The University
            of Queensland, QLD 4072, Australia.
            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..5209
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="U13A"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pU13A_C"
                     /geo_loc_name="USA:Utah"
                     /collection_date="2013"
     gene            complement(join(5100..5209,1..247))
                     /locus_tag="U13A_RS26730"
     CDS             complement(join(5100..5209,1..247))
                     /locus_tag="U13A_RS26730"
                     /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="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_240145044.1"
                     /translation="MGVMIPMKRERMLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGE
                     PVARSGRLPTLAPPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRR
                     LRLAVREQGTRDDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            279..470
                     /locus_tag="U13A_RS26735"
                     /old_locus_tag="U13A_C00001"
     CDS             279..470
                     /locus_tag="U13A_RS26735"
                     /old_locus_tag="U13A_C00001"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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_000165988.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDSENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1138..1251
                     /locus_tag="U13A_RS27920"
     CDS             1138..1251
                     /locus_tag="U13A_RS27920"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001422066.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001427889.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLAAAIGN"
                     /name="hypothetical protein"
     gene            1658..2047
                     /locus_tag="U13A_RS26750"
                     /old_locus_tag="U13A_C00003"
     CDS             1658..2047
                     /locus_tag="U13A_RS26750"
                     /old_locus_tag="U13A_C00003"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001679965.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000477210.1"
                     /translation="MFKSSVKSITSSTILTLLIGCSSTETNKNIVYKVGGDSIILNKYC
                     ILKMYPSQSEKNKGVIIEVNTDSLCKKKLNEITSKNIGKPLISYFDGKVISQPAIIHSA
                     LNPTHYYQPVNDETTVMEIIKAYSK"
                     /name="hypothetical protein"
     gene            complement(2111..2395)
                     /locus_tag="U13A_RS26755"
                     /old_locus_tag="U13A_C00004"
     CDS             complement(2111..2395)
                     /locus_tag="U13A_RS26755"
                     /old_locus_tag="U13A_C00004"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000625497.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin Z C-terminal domain-related protein"
                     /protein_id="WP_000625497.1"
                     /translation="MISQNVWAPPFFFGPWVELENHTGDIAYTVYFDTLSNVPGPFIAF
                     IWYAPNGPRTVNVIGPASYQISCKGAGVDKIKFKSVSGTGQIIHVYTTL"
                     /name="colicin Z C-terminal domain-related protein"
     gene            complement(2413..2610)
                     /locus_tag="U13A_RS26760"
                     /old_locus_tag="U13A_C00005"
     CDS             complement(2413..2610)
                     /locus_tag="U13A_RS26760"
                     /old_locus_tag="U13A_C00005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335786.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001335786.1"
                     /translation="MKEEKVLLHRFLFVVRNKNGCELSCSADLMGTRDDVYKYFSDSVS
                     GLDVELIDVSCESEWEEHSH"
                     /name="hypothetical protein"
     gene            2822..3118
                     /locus_tag="U13A_RS26765"
                     /old_locus_tag="U13A_C00006"
     CDS             2822..3118
                     /locus_tag="U13A_RS26765"
                     /old_locus_tag="U13A_C00006"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001679964.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000047647.1"
                     /translation="MSKTKSGRHRLSKTDKRLLAALIAAGYEERTARDLIQKHVYTLTQ
                     ADLRHLVSEISNGVGQSQAYDAIYQARRIRLARKFLNGKKPEEGLNAWKGDLP"
                     /name="hypothetical protein"
     gene            complement(3665..3898)
                     /locus_tag="U13A_RS27020"
     CDS             complement(3665..3898)
                     /locus_tag="U13A_RS27020"
                     /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_001555310.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWESAFVELQKMFSLTQRDNA
                     MLNERVMKLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(3905..4423)
                     /locus_tag="U13A_RS27025"
     CDS             complement(3905..4423)
                     /locus_tag="U13A_RS27025"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001447511.1"
                     /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_023144181.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETILNDEFRKLEKSVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVIFLFTVSC
                     GTLWYLGGMIQANLEDIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVIPHQ
                     GKDWVQLME"
                     /name="MbeB family mobilization protein"
     gene            complement(<4461..4892)
                     /locus_tag="U13A_RS27030"
                     /pseudo=""
     CDS             complement(<4461..4892)
                     /locus_tag="U13A_RS27030"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /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"
     Typing          complement(556..643)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.86e-39"
     Typing          654..1210
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(3..247)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.78"
                     /coverage="99.0"
                     /evalue="2.3e-46"
     Typing          complement(3562..5093)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.262"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 actgtccgct gttcacctta cgggctgtct ggttcaggtt attcccgatg gctgccagct
       61 gacgcagtaa cggcggtgcc agtgtcggca gcctcccgga acgggcaacc ggctcaccca
      121 ggcagacccg ccgcatccat accgccagtt gtttaccctc acagcgttcc agtaaccggg
      181 catgttcatc atcagtaacc cgtatcgtga gcatcctctc gcgtttcatc ggtatcatta
      241 cccccatgaa cagaaatccc ccttacacgg aggcatcagt gactaaacag gaaaaaaccg
      301 cccttaacat ggcccgcttt atcagaagcc agacattaac gctgctggag aagctcaacg
      361 aactggacgc ggatgaacag gcagatatct gtgaatcgct tcacgaccac gccgatgagc
      421 tttaccgcag ctgcctcgcg cgcttcgggg atgacagtga aaacctctga catatgcagc
      481 tcccggagac ggtcacagct tgcctgtgag cggatgccgg gagcagacaa gcccgccagg
      541 gcgcgtcagg gtgttttagc gggtttcggg gcgcagccct gaaccagtca cgtagcgata
      601 gcggagtgta tactggctta accatgcggc atcagtgcgg attgtatgaa acgtgcgcca
      661 taccgggtgt gaaatgccgc acagatgcgt aaggagaaaa tgcacgtcca ggcgcttttc
      721 cgcttcctcg ctcactgact cgctacgctc ggtcgttcgg ctgcggcgag cggtatctac
      781 tcactcaaaa acgaaatgct gttatccaca gaatcagggg ataacaccgg aaaaaacatg
      841 tgagcaaaag accaggaaca ggaagaaggc cgcgccgctg gcgtttttcc ataggctccg
      901 cccccctgac gagcatcaca aaaatcgacg ctcaagtcag aggtggcgaa acccgacagg
      961 acttaaagat accaggcgtt tccccccgga agctccctcg tgcgctctcc tgttccgacc
     1021 ttaccgttta ccggatacct gtccgccttt ctcccttcgg gaagcgtggc gctttctcat
     1081 agctcacgct gtaggtatct cagttcggtg taggtcgttc gctccaagct gggctgtgtg
     1141 cacgaacccc ccgttcagcc cgaccgctgc gccttatccg gtaactatcg tcttgagtcc
     1201 aacccggtaa gacacgactt aacgccactg gcagcagcca ttggtaacta aaaagtggat
     1261 ttagatacgc agaactcttg aagttgaagc cttatagcgg ctacactgaa aggacatctt
     1321 ttggtatctg tgctccactt aagccagcta cccggttagg taatctgcca ggattagcta
     1381 accttcgaaa aaccacctgc cagggtggtt ttttcgttta caggcagcag attacgcgca
     1441 gaaaaaaagg atctcaagaa gatcctttga tctttttttc tctaaactgc aatcccatca
     1501 gttcaggaga gaaagatagt ataattgccc tctcttatat ggaaccacca ttcaatcaca
     1561 tcatggggat aatataagtg aaaacgttcg cattgtttat ttttacgtgt atatgtattt
     1621 atagattgga attttaacaa aataaaatgg agttaatatg ttcaaatcat cagtaaagtc
     1681 aataacatcg agtactatac tgaccttact tataggatgt tcaagtactg aaacaaacaa
     1741 aaacattgtt tacaaagttg gtggtgacag catcattctg aataaatatt gcatacttaa
     1801 aatgtaccct tcccaatcag aaaaaaacaa aggcgtcata atagaagtaa acacagatag
     1861 tttatgtaag aaaaaactaa acgaaataac tagtaaaaat atagggaaac ccctgatttc
     1921 atattttgat ggaaaagtaa tatcccaacc tgcaatcatt cattctgcac taaatccaac
     1981 ccattattat caacctgtga acgatgaaac aacagtgatg gaaatcataa aagcatattc
     2041 aaaataatat taatagatat aatcctgctt aaggtatagc ttaggcagga ttatatttat
     2101 tcagctctta ttataaggta gtgtatacat gaataatctg ccctgtccca ctgacacttt
     2161 taaatttaat tttatcaaca ccagcgccct tgcaagagat ctgataagat gctggaccaa
     2221 taacgttaac tgttcttggc ccattagggg cataccagat aaaagcaata aatggaccgg
     2281 gtacattaga caatgtatca aaatagacag tgtacgcgat atcaccagta tgattttcaa
     2341 gttcaaccca aggaccaaaa aagaaaggag gagcccaaac attttgagaa atcatataat
     2401 ctcctgatta gttcaatgcg aatgttcttc ccattcactc tcgcaagaaa catctataag
     2461 ctcaacatct agcccactaa cagaatcaga gaaatactta taaacatcat cccttgttcc
     2521 cataaggtct gccgaacatg atagttcaca accattctta ttcctaacta caaataagaa
     2581 acggtgaagc aatacttttt cttctttcat tttatccctc cctttattta cacagaatat
     2641 actgtatata taaatactag ttttatatac agtataaatt acgccgcatt atttttcctg
     2701 tcaatgatat gaattttcat ttttgtgatc tgaatcaccc ttataaaaat caggaaggga
     2761 agattcgcag cagaaaaaca gcaccggata acatcaggag aaaaaacaga gaggagataa
     2821 cgtgagcaaa acaaaatctg gtcgccaccg actgagcaaa acagacaaac gcctgctggc
     2881 tgcacttatc gctgccggat acgaagagcg gacagcccgt gacctcatcc agaaacacgt
     2941 ttacacactg acacaggccg acctgcgcca tctggtcagt gaaatcagta acggtgtggg
     3001 acagtcacag gcctacgatg cgatttacca ggcaagacgc attcgtctcg cccgtaaatt
     3061 cctgaacgga aaaaaaccgg aagaagggct gaacgcctgg aagggtgatt taccataatc
     3121 acttattgta cgcaccgccg aaacgcgttc ggtgcgatca cggcagcaga caggtaaaaa
     3181 tggcaacaaa ccacccggaa aactgccgcg atcgcacccg gtaaatttta accacatgca
     3241 tacctatgca gccaggtgaa tcacgcagga attgccagtc agagaccgct gaaacggatt
     3301 tttttcatac tttcggaagc gaagaagacg gggatttgag caggaaaaca gaagttcagg
     3361 ggaatgagcg cgatctggca atagaggcaa aaacacgact atgaaagaca caccagaatc
     3421 gcgcccgtat gcgttttaac gcgttcctgt gttttcagca aggtttatga ctgaagcgcg
     3481 ttcccggtgc cccgaaccaa ccattatccc aaaaaatgca ccggaaacgc gctgacaaca
     3541 ttttagcctg tctctgatta ccatcccagc gaagggccat ccagtgtccg ttcctgtatt
     3601 tccagctggc gctcacgctc cagggataac tcatgttcgc gttcctgtat cagccgttcg
     3661 tcccttatct cctgttctcg ctgtataact ggctcaagcg ttctgtccgc tcgctcaagt
     3721 gctgcacctg ctgactcaac ttcatgaccc gctcgttcag catcgcgttg tcccgttgcg
     3781 taagcgaaaa cattttctgc aattccacga aggcgctctc ccattcgttc agccgctgca
     3841 tatagtcctg ttgcagttgc tctaatgcgt tcagcaaatg tctttccagc tccgtcactc
     3901 tgtgtcactc catcagttgt acccagtcct tcccctgatg gggaatcacc tctgctgatt
     3961 tcccgtacgg aaggaccaga aatttcctgt tcccgtcctg tacgaactcc acgccccatg
     4021 tcttcgcgtt cagtttctgc aatgtctctt cctgcttcct gatatcttcc aggttcgcct
     4081 gtatcatccc gccaagatac cagagcgtcc cgcaactcac ggtaaacagg aaaatgacca
     4141 tccccagtaa catcatgccc gtattccctg ccagctttaa cacgtccttc ctgtgctgca
     4201 tcatcgcctc tttcacccct tcccggtgct ttttcagtga ttcctctgtc gaagctgtga
     4261 acagggctat agcgtctttg attttcgtct cgtttgatgt cacagccttg cttacagatt
     4321 tttcgagctt cctgaactcg tcgttcagta ttgtctctgt agattcggct ctctctttca
     4381 gctttttctc gaactccgcg cccgtctgta aaagattgct cataaaatgc tcctttcagc
     4441 ctgatattct tcccaccgtt cgggtctgca atgctgatac tgcttcgcgt caccctgacc
     4501 acttcaagcc ctgcctctgt gagcgcctga atcacatcct gacggccttt tatctccccg
     4561 acatgataaa gagcgtctat cccgcgtgtg acgctctctg caagcgcctg tttcgtttcc
     4621 ggcaggttat cagagagagt cagtatccgg cggttctccg gggcgttggg gtcatgcagc
     4681 ccgtaatggt gattcaccag cgtctgccag gcatcaattc tcggcctgtc tgcccggtcg
     4741 tagtacggct ggaggcgttt tccggtctgt agctccatgt tcggaatgac aaaattcagc
     4801 tcaagccgtc ccttgtcctg gtgctccacc cacaggatgc tgtactgatt tttttcgaga
     4861 ccgggcatca gtacacgctc aaagctcgcc atcacttttt cacgtcctcc cggtggcagc
     4921 tccttctccg cgaacgacag cacaccggac gtgtatttct tcgcaaatgg cgtggcatcg
     4981 atgagttccc gtacttcttc cggattaccc tgaagcaccg ttgccccttc ccggttacgc
     5041 tcccttccca gcaggtaatc aaccggacca ctgccaccac cttttccccg gcatgaaact
     5101 taactatcat cccgcgtccc ctgttccctg acggccagac gcaaccggcg cagctcatcc
     5161 ccgatggcca tcagtgcggc caccacctga acccggtcgc cggaagacc
//
