LOCUS       CP054453                1591 bp    DNA     circular BCT 14-JUN-2020
DEFINITION  Escherichia coli strain SCU-488 plasmid pSCU-488-4, complete
            sequence.
ACCESSION   CP054453
VERSION     CP054453.1
DBLINK      BioProject: PRJNA624897
            BioSample: SAMN14943542
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1591)
  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  JOURNAL   Unpublished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 1591)
  AUTHORS   Stephens,C., Arismendi,T., Wright,M., Hartman,A., Gonzalez,A.,
            Gill,M., Pandori,M. and Hess,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-JUN-2020) Biology, Santa Clara University, 500 El
            Camino Real, Santa Clara, CA 95054, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Flye v. 2.6
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 44x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/04/2020 19:12:22
            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)                     :: 5,111
            CDSs (total)                      :: 4,995
            Genes (coding)                    :: 3,821
            CDSs (with protein)               :: 3,821
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 1,174
            CDSs (without protein)            :: 1,174
            Pseudo Genes (ambiguous residues) :: 0 of 1,174
            Pseudo Genes (frameshifted)       :: 1,057 of 1,174
            Pseudo Genes (incomplete)         :: 111 of 1,174
            Pseudo Genes (internal stop)      :: 69 of 1,174
            Pseudo Genes (multiple problems)  :: 60 of 1,174
            CRISPR Arrays                     :: 2
            ##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..1591
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-488"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-488-4"
                     /geo_loc_name="USA: California"
                     /collection_date="2018"
     gene            complement(486..961)
                     /locus_tag="HPE47_25550"
                     /pseudo=""
     CDS             complement(486..961)
                     /locus_tag="HPE47_25550"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000469298.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /name="helix-turn-helix domain-containing protein"
     gene            1464..1589
                     /locus_tag="HPE47_25555"
     CDS             1464..1589
                     /locus_tag="HPE47_25555"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001431667.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication protein"
                     /protein_id="QKP94443.1"
                     /translation="MWLPVLFRFLVDSLATLGHRLAASGITSRMLSVIPVLFFWG"
                     /name="replication protein"
     Typing          1041..1149
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.182"
                     /coverage="100.0"
                     /evalue="4.23e-47"
     Typing          complement(1345..1443)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.22e-45"
     Typing          2..255
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.765"
                     /coverage="97.0"
                     /evalue="1.44e-95"
ORIGIN
        1 gcatgttgtc ggtgatcccg gtgttgttct tttggggatg agtcgccaga tagcccctca
       61 aacgcgctca aaagctctca gacgcacgaa acgggtttta gatgcccgcc agggcatgga
      121 aggcgcgaaa aacgcttaca gaggctctca ggaggtcaag cgcgccgata cccctaacca
      181 ggggctttca ggtcgccagg aaccgcgcca gccccctgca aagcccattt gcacggaaca
      241 ggcagccatg cggttggtag gtggtcgtag accgtcggtg ttgcagcgat gggggtctgg
      301 ggttctcccc agacggtttc cggtagcgct caaggcgctg ccggaaccgt ggcggctcgg
      361 ttttttctgg agaacgggga gcaaaaacac gcaaaggatt ttgaggcggc aaaagagcaa
      421 tgcaggatag acaatcatgg tcagaacgtt aacacgtagc ccctgattgt ccgcctgccg
      481 ctagctcaat ttgaaaacat ggccatgatt cggcgctgaa tatcaccgtc tttgttgacc
      541 agtgttttag tgacaaacgc tgcatggttt cgtagtgttg tatcccttcc agacttcatg
      601 tggatcgagg gcatacgcac aaaccttacc agcaacgggg gattctaact aatgcatttt
      661 ttgattctaa gtaattgagc caccgaataa ttgtgcttct gctaactcca agtttttcag
      721 ctaggaattg ctgatccgca acgacagcgc cacacgtagg atcgatatgc tccgctaaaa
      781 atgagtacag cttcagtgct gatatgcctt ggctatcctt cagcagctct cgaacacgtt
      841 cccaaccttt tggggatacc tgtgtaaacc ttgaattttt ctttgcttct tcgagatcct
      901 cggtgttttt ctttgcctca tctgaaagtt gtttcagtcg tttttctgaa tcaataaaca
      961 tgattttttc cctctgaaaa tcccatgcac taacgttggt tcaaatctaa gccatcatga
     1021 cacatctgtg caacaccttg ttgcgtgttg tcgcatccag gatgcgacaa cgttgtgtca
     1081 tccaggatgc gacaggtaaa taaaaaacac actaaaaaaa caaccactta caaatcggcg
     1141 taaaagatct attctaggca agggtgttgc gtgcaacgca acgccctttg gaggtgtcgg
     1201 ggcgaagccc tgacccagtc acgtagcgat agcggagtgt atactggctt actcctatgc
     1261 aagcctcgcc agccgtgatt tttgccagat ttcgtggttt tcacgttcaa cagctccatc
     1321 gtgtttttgc cgtccgttca ccgttaaaac gcctcagaaa tcgggacagg atgtgtaatc
     1381 gtataaccgc gcatgcacgc cgatacgatt accacttggt cagggcttca ccccgacacc
     1441 ccgcatcagt gcgtaagtgc tcaatgtggc ttccggttct cttccgcttc ctcgtcgatt
     1501 cgctcgctac gctcggtcat cgacttgcgg cgagcgggat cacctctcgc atgttgtcgg
     1561 tgatcccggt gttgttcttt tggggatgag t
//
