LOCUS       CP054462                3182 bp    DNA     circular BCT 14-JUN-2020
DEFINITION  Escherichia coli strain SCU-103 plasmid pSCU-103-5, complete
            sequence.
ACCESSION   CP054462
VERSION     CP054462.1
DBLINK      BioProject: PRJNA624897
            BioSample: SAMN14943534
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3182)
  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  JOURNAL   Unpublished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 3182)
  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, Unicycler v. 2.6, 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 57x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/04/2020 20:11:23
            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)                     :: 5,482
            CDSs (total)                      :: 5,353
            Genes (coding)                    :: 3,705
            CDSs (with protein)               :: 3,705
            Genes (RNA)                       :: 129
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 92
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 1,648
            CDSs (without protein)            :: 1,648
            Pseudo Genes (ambiguous residues) :: 0 of 1,648
            Pseudo Genes (frameshifted)       :: 1,488 of 1,648
            Pseudo Genes (incomplete)         :: 174 of 1,648
            Pseudo Genes (internal stop)      :: 59 of 1,648
            Pseudo Genes (multiple problems)  :: 68 of 1,648
            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/
            NCBI analysis of this genome has determined that >30% of the
            predicted CDS features contain frameshifts, which is well above the
            usually observed value of <10%.
FEATURES             Location/Qualifiers
     source          1..3182
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-103"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-103-5"
                     /geo_loc_name="USA: California"
                     /collection_date="2015"
     gene            complement(318..431)
                     /locus_tag="HPE39_27380"
     CDS             complement(318..431)
                     /locus_tag="HPE39_27380"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="QKQ01917.1"
                     /translation="MHEPPVQSDYHARSGNYQLESNPERHDKSPVAVAIGN"
                     /name="replication initiation protein"
     gene            2165..2632
                     /locus_tag="HPE39_27385"
     CDS             2165..2632
                     /locus_tag="HPE39_27385"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014605173.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="QKQ01918.1"
                     /translation="MSDTNKFRSLRLARAWSQEQLAELSGMSVRTVQRIENGDQPSLET
                     LSALAAVFEVSVADLSGPDAHGDDALDQKIAEAKSKIAEEGRFYRSVITAVVVCALLLV
                     LNHFTAPASAWSFWVAGIWCALLVIRGMRTFVLRGLISRWQQKRLRRMLRR"
                     /name="helix-turn-helix domain-containing protein"
     gene            2644..3144
                     /locus_tag="HPE39_27390"
     CDS             2644..3144
                     /locus_tag="HPE39_27390"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017456310.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QKQ01919.1"
                     /translation="MDIADFLRNTPVWVWILLAFLLRRGFAALYDREMTTGRLFFLPIL
                     FLVWGAYGVITETKLAGVSLTMMTAGLLVGTALGYRLWRSQPPLRNSDNPGMIIRAGTP
                     LTLGLIVITFCMKFILVSVIDLHPGLRSSAIFCMLFGGVTGLVDGVFWGGTLRLFIPWY
                     SKR"
                     /name="hypothetical protein"
     Typing          complement(319..803)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.187"
                     /coverage="93.0"
                     /evalue="7.71e-161"
ORIGIN
        1 tttcatcggc catcccaaaa ccctgatttt acgatctatg aaataggccg gtttaatctt
       61 caaacgcctt catggatgaa gacgataatc gctcctgtaa aaaggatctt cttgagatcc
      121 tttttttctg cgcgtaatct cttgctctga aaacgaaaaa accacctggg gaggtggttt
      181 gatcgaaggt taggtcagtt ggggaactgc ttaacctggt aactgtcttg tgcgagacga
      241 gtcacctaaa ctgtccttcc agtgtagccg cactcaggcc cccacttcaa gaactccaga
      301 taaatctctc gcacatctca gttaccaatg gctaccgcca ctggcgattt gtcgtgtctt
      361 tccgggttgg actcaagttg atagttaccg gaacgggcgt ggtagtcgga ctgaacgggg
      421 ggttcgtgca tacagtccag cttggagcga actgcctacc cggaactgag tgtcaggcgt
      481 ggaatgagac aaacgcggcc ataacagcgg aatgacaccg gtaaaccgaa aggcaggaac
      541 aggagagcgc acgagggagc taccaggggg aaacgcctgg gatctttata gtcctgtcgg
      601 gtttcgccgc cactgatttg agcgtcagat ttcgtgatgc ttgtcagggg ggcggagcct
      661 atggaaaaac ggctacgccg catccttttt ccggtccttc atgatttgag cactgcctgc
      721 gtatcccgtt atttgtgagc cggtaacgcc cgccgcagtc tcacggcagg agcgtagcga
      781 ccgagtgagc gaggaggcgt catttcacct ttacctacat gttgcactta cgcacgatag
      841 ccacattttt cctttgccac atgaagcact tccctgaatt accactccga tttaacatat
      901 taagccagta tacactccgc tatcgctacg tgactgggtc atggctgcgc cccgacaccc
      961 gctaaaaccc gctgacgcgc cctgacgggc ttgtcggctc ccggcatccg ctcacaggca
     1021 agctgtgtcc gtctccggga gctgcctgta tcagcccgtt atgccatcat cgccgaagcg
     1081 ttcccggcaa cgttggtagc gttcatccgc cacttcgtga agttgttctg gtgaaaaaaa
     1141 cacgtacagg acggggcagg atgtgcattt gtcggaccgc gcacgcgcaa tcagacaaat
     1201 gccacctggt cagggcacag ccccgacacc ctggacaaca ccaaagcaat aagataaaac
     1261 gtacctgggc gcgtttctct gcctcttttt tcatcatctc tgggattcgc gctcacccgt
     1321 cctctgctgt cgggtttatg tatccccgtc gcccgtggag atgaataacg ggccggggga
     1381 ttaaaaatcc ccgtgccgca cagccagcgt tgcataaaat tccgctctgc ggtgactatt
     1441 gtttaatcaa aaatccccgc tgttcctcca gaaaaacgcg agtctgttct cattcccagg
     1501 atgcccacac cccacgcaaa actaactttt ttctgatttg ttttttaaat catgttgtta
     1561 tggtttgaaa aatatatttt cttattcgga tttatacaaa agcggctcgt cggcgactac
     1621 tggatgactc ggcaacgagt cgtcggtgat ttatcgatga ctcaacacac tgtcgctctg
     1681 gtgttcagag aaggcgagtc gccagagagt cgcgaggaaa aatactggat gactcgccga
     1741 cgactcccgt agtgaatcgc tcacgactcg tctgtaacta cagtctgatt tcttcttatc
     1801 agggctgaaa acgtccgaaa atacgcctta tgggcatcag acgcgcccaa accgatcgcc
     1861 attcagtttc atgcatagtc atgcaacgcg ctgaaagcgt tcctgacgca tttttccggt
     1921 ttacccgggg gaaaacatcc atttttacgg tttttgcgcc agaagcgcgc tgagcgcgtt
     1981 ttaacggtgc gtacaatgaa ctcttatgtt aaatctgacc gtacatgctt ctgaagttac
     2041 ggtttcaaag acctcaatgc ggcatgtcag accgctgtca cgttactgtc gggttaagat
     2101 cgtggtcgcg caggattacg cggtcaacac tgtgtgctga ccatcttcca ttcggagaca
     2161 ggaaatgagt gataccaaca aattcaggtc gctgcgtctt gcgcgtgcct ggtcccagga
     2221 gcagcttgct gaactgtccg ggatgagcgt gcgcacggtt cagcgtatcg agaacggcga
     2281 tcagccaagc ctggaaacac tgagtgccct ggctgctgta tttgaggtga gcgtggcgga
     2341 tctttccggc cctgatgcgc atggcgatga cgctcttgac cagaaaattg ccgaagcgaa
     2401 gagcaaaata gctgaggaag gccgttttta ccgatcagta attacggctg tcgtcgtctg
     2461 cgcgctgttg cttgttctta accactttac ggccccggcc agcgcatggt cattttgggt
     2521 tgcggggatc tggtgtgcgc tgctggttat tcgtggcatg agaacgttcg ttttgcgcgg
     2581 gctgatcagc agatggcaac agaaacgact gaggcggatg ctgcggcgat aatgggaata
     2641 cttatggata ttgcagactt tttacgaaat acccccgtct gggtatggat cctgctggct
     2701 tttttactac gacgcggttt tgctgctctt tatgaccggg agatgacaac cgggcgtttg
     2761 ttttttctcc cgatactttt ccttgtatgg ggagcatatg gtgttatcac tgagacaaaa
     2821 cttgctggcg taagccttac aatgatgacg gcaggactgc tcgtaggcac cgctcttgga
     2881 tacaggttgt ggcgctcaca gcccccgctg agaaattcag ataatccggg catgattatc
     2941 agggccggga caccgctgac tttgggactg attgtaatta ctttttgcat gaagtttata
     3001 cttgtctcag tcattgatct gcaccccgga ttacggtcat ccgcaatttt ttgcatgtta
     3061 tttggcggtg tgacaggact tgttgatggc gtattctggg gtggaaccct gagacttttc
     3121 ataccctggt acagcaaaag atgattgtta gtaggtgtat gtatttatgg gtttttatgg
     3181 gg
//
