LOCUS       NZ_CP054360             2311 bp    DNA     circular CON 13-JUN-2023
DEFINITION  Escherichia coli strain SCU-172 plasmid pSCU-172-7, complete
            sequence.
ACCESSION   NZ_CP054360
VERSION     NZ_CP054360.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14943545
            Assembly: GCF_013315695.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2311)
  AUTHORS   Stephens,C., Arismendi,T., Wright,M., Hartman,A., Gonzalez,A.,
            Gill,M., Pandori,M. and Hess,D.
  TITLE     Title: F plasmids are the major carriers of antibiotic resistance
            genes in human-associated commensal E. coli
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2311)
  AUTHORS   Stephens,C., Arismendi,T., Wright,M., Hartman,A., Gonzalez,A.,
            Gill,M., Pandori,M. and Hess,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (18-MAY-2020) Biology, Santa Clara University, 500 El
            Camino Real, Santa Clara, CA 95054, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 78x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/13/2023 03:55:40
            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)                     :: 5,461
            CDSs (total)                      :: 5,339
            Genes (coding)                    :: 5,056
            CDSs (with protein)               :: 5,056
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 94
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 283
            CDSs (without protein)            :: 283
            Pseudo Genes (ambiguous residues) :: 0 of 283
            Pseudo Genes (frameshifted)       :: 85 of 283
            Pseudo Genes (incomplete)         :: 198 of 283
            Pseudo Genes (internal stop)      :: 39 of 283
            Pseudo Genes (multiple problems)  :: 33 of 283
            Pseudo Genes (short protein)      :: 3 of 283
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP054360.1.
            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..2311
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-172"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-172-7"
                     /geo_loc_name="USA: California"
                     /collection_date="2017"
     gene            677..1174
                     /locus_tag="HPE50_RS26945"
                     /old_locus_tag="HPE50_26955"
     CDS             677..1174
                     /locus_tag="HPE50_RS26945"
                     /old_locus_tag="HPE50_26955"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001027759.1"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA];
                     GO:0006276 - plasmid maintenance [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="WP_001027759.1"
                     /translation="MNITERTDSKKKVLRQNITEVIDRETGNITQEITDITVQFPQEPA
                     YVKIYIDNLCAVTKAPDSLKDVLFLILRKLDYDGYIALSTRYRKEICKLLGIKDGTLRN
                     RLYSLSKMGIIASCGGNEYQANPNLFARGEWKKIIEQRREFEMRIKYSPNGETIITTEE
                     IK"
                     /name="replication/maintenance protein RepL"
     gene            complement(1208..1633)
                     /gene="mobA"
                     /locus_tag="HPE50_RS26950"
                     /old_locus_tag="HPE50_26960"
     CDS             complement(1208..1633)
                     /gene="mobA"
                     /locus_tag="HPE50_RS26950"
                     /old_locus_tag="HPE50_26960"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001107325.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_001107325.1"
                     /translation="MAKNKRSGSEVRQRTKVITLRVNNRVASEIRRRAKNEGLTISEYI
                     RTASLNNEIKQRVPSRYLDELIRLGRMQKKLFDKGKRPKDKEYLEVMHKIILLCDEMKI
                     VTKRISDVYNEMDLIKDEIKIIKRIHKNKYPGSDLFK"
                     /name="mobA"
     Typing          complement(68..326)
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.218"
                     /coverage="100.0"
                     /evalue="3.19e-77"
ORIGIN
        1 cgaaaccgtc tggggagaac cccagacccc caccgctgca acatcatcgg tctacgacca
       61 cctagcaacc gagtggctac ctgtgccgtg caaacaggct ttgcaggggg ctggcgcggt
      121 tcctggcgac ctgaaagccc ctggttaggg gtatcggcgc gcctggcctc ctgaaaccct
      181 ctgtaagcgt ttttcgcgcc ttccatgccc tgacgggcat ttagaccccg tttcgtgcgt
      241 ctgggaggct ctgagcgcgt ttaacagatg accagcgact cgatcgcctg agatcaaatc
      301 gggatcatca acgatatgcg agaggtggca ccgctcgccg cagccccagc gaccgagccg
      361 ccaggctcgc gagtgggcga ggaagcggaa gagaaccgga agctacattg agcacgcacg
      421 ctcaatatta aaattgtcac ttcgtaaata gagattatgc ctcgtgctta tggatacatt
      481 taaaaatata agatatccga attaggctac atacgggctg atcgccaatg ttgtaacgtg
      541 tagaagatac acctgtaacg tgtacaggat actcctgtaa cgtgtgggcg gtattcccgt
      601 aatctatatt gagtgacatt ttgttttttg ggcattatat tgtctgtcac ctttataaag
      661 tgacaaaggc gataaaatga acattactga aagaacggat agcaagaaaa aagttttaag
      721 acaaaatatt actgaggtta tagatagaga aactggaaac ataacacaag aaataaccga
      781 tataacagtt caatttccac aagaacctgc gtatgtgaaa atttatattg ataatttatg
      841 tgctgtcaca aaagcacctg attctctaaa agatgtttta tttttaattc ttaggaaatt
      901 ggattatgac ggatatattg cattatcaac tagataccgt aaggagatct gtaaattatt
      961 gggaataaaa gacggaacat tacgtaacag attgtattca ttatcaaaaa tggggattat
     1021 tgctagttgt ggcggtaatg aatatcaggc gaaccctaat ttatttgctc gtggtgaatg
     1081 gaaaaaaata attgaacagc gtcgcgagtt tgaaatgaga attaaatatt cacctaacgg
     1141 tgaaactatt ataacaaccg aagaaataaa ataatgtgca cctaaataag gtctttttaa
     1201 aaagacctta tttgaataaa tccgaacctg gatatttatt tttatgtatc ctttttatta
     1261 tttttatttc atcctttatt aaatccattt cattatatac atcagaaatt cgcttcgtta
     1321 ctattttcat ttcatcgcaa agtaaaatta ttttatgcat cacctcgagg tactccttat
     1381 ccttcggccg ctttccctta tcaaataatt tcttctgcat ccgaccaagt cggattaatt
     1441 catctaaata cctggaaggt acgcgctgtt ttatttcatt atttaaactt gccgtcctga
     1501 tatattctga aattgtcagt ccttcgttct tcgctcgccg tctgatttcg cttgcgactc
     1561 tgttatttac tctaagggtg ataaccttag ttctctgccg tacttctgaa ccactacgtt
     1621 tatttttagc catcgcaatg actctccatt ttgcacgttt ggggtgtcgg ggcttgccct
     1681 gacaggaggt attctcatgc aagcgaatgt attcgcggta tgacgaatac acatcctgtc
     1741 caattttccg ctacaacttt tcgacgaaaa taaaataccg cgtcgtaacc tggtatttct
     1801 gatacaaaaa aatgatgcat cattcaatat tatttacaca gattttaaaa ttattgcttg
     1861 ttatttaata aataacatcg aattaattga tgtctttgtt gtctgtcgtt tgtggattat
     1921 tagagtgata aagattagat cttcctcgtt atataatcca ttgcctgtta atgatacgga
     1981 gtgagtccaa ggaacaggaa gcggaagagc aagatagtag catgtacata aaatataaat
     2041 ccgtgagtta ttgatatcgc gtttatatat taaaaatata acttaacatt gctcttaata
     2101 tttattttgt cctggcaatg ggagcattaa tccccgtgca gtgctccgcc agctgctgac
     2161 aacctcgaca tataaccatc gatacgatag aacatcaggg cgcgtttccg gcaagaacta
     2221 accatgggga tggtttgcgt gccgacaaac gccggaacgc gcctcaaatc caccaagccg
     2281 ccacggttcc ggcagcgcct tgagcgcaac c
//
