LOCUS       CP054333                3749 bp    DNA     circular BCT 10-JUN-2020
DEFINITION  Escherichia coli strain SCU-121 plasmid pSCU-121-5, complete
            sequence.
ACCESSION   CP054333
VERSION     CP054333.1
DBLINK      BioProject: PRJNA624897
            BioSample: SAMN14609781
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3749)
  AUTHORS   Stephens,C., Arismendi,T., Wright,M., Gonzalez,A., Gill,M.,
            Hartman,A., Pandori,M. and Hess,D.
  TITLE     F plasmids are the major carriers of antibiotic resistance genes in
            human-associated commensal E. coli
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3749)
  AUTHORS   Stephens,C., Arismendi,T., Wright,M., Gonzalez,A., Gill,M.,
            Hartman,A., Pandori,M. and Hess,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-MAY-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                   :: 12x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 05/26/2020 18:38:34
            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)                     :: 4,901
            CDSs (total)                      :: 4,791
            Genes (coding)                    :: 3,570
            CDSs (with protein)               :: 3,570
            Genes (RNA)                       :: 110
            rRNAs                             :: 7, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 1,221
            CDSs (without protein)            :: 1,221
            Pseudo Genes (ambiguous residues) :: 0 of 1,221
            Pseudo Genes (frameshifted)       :: 1,095 of 1,221
            Pseudo Genes (incomplete)         :: 102 of 1,221
            Pseudo Genes (internal stop)      :: 95 of 1,221
            Pseudo Genes (multiple problems)  :: 67 of 1,221
            ##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..3749
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-121"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-121-5"
                     /geo_loc_name="USA: California"
                     /collection_date="2016"
     gene            join(3729..3749,1..498)
                     /locus_tag="HHJ34_24480"
     CDS             join(3729..3749,1..498)
                     /locus_tag="HHJ34_24480"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221101.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QKN43418.1"
                     /translation="MRFLLILRISTEDTPCTRRPQAIYCTTTTHRKKTPGSTTNMRISN
                     IEWLKKRIGFIRKLGEQTARQRQIIDLLDNEAGLTEQERKLLHVLATAEKNDLQAQESE
                     RKQAVQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTGELCYKKDRILQALKEIKYD
                     LETSPNPDA"
                     /name="hypothetical protein"
     gene            complement(758..1777)
                     /locus_tag="HHJ34_24485"
     CDS             complement(758..1777)
                     /locus_tag="HHJ34_24485"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221104.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid replication protein"
                     /protein_id="QKN43419.1"
                     /translation="MSAALQYFEENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWQVMEWREDAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLEAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGKANSSENQSDKGKKS
                     AAVRWTANDDKRRRALDMYILGASTEDIAVAVGVSSRTIRRWMDNSGEWLTKKQIIKC"
                     /name="plasmid replication protein"
     gene            complement(2210..2743)
                     /locus_tag="HHJ34_24490"
     CDS             complement(2210..2743)
                     /locus_tag="HHJ34_24490"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221103.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QKN43420.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQKLDVAGLIGERISQDFQRLEESVANMKANADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFCVLGWGMKTMLDRNYNATAAVYQKVVTLED
                     KLAEKPVTGKSRKN"
                     /name="hypothetical protein"
     gene            complement(2746..3672)
                     /locus_tag="HHJ34_24495"
     CDS             complement(2746..3672)
                     /locus_tag="HHJ34_24495"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221102.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="QKN43421.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTAEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIDGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     LTQQKEQLRELRKRWEVKHNEHMRKHGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGYDIREWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQNRTEPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     Typing          complement(1003..1777)
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.907"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          complement(2750..3672)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.727"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cgaattagca cggaagatac cccctgcacc cgccgaccgc aagcgatata ctgcacgacc
       61 acaacacacc gcaaaaaaac accagggagc accacgaaca tgcgcatcag caacatcgaa
      121 tggctgaaga aacggatcgg attcatcagg aagctcggag aacagaccgc acgacagaga
      181 cagattattg acctgctcga caacgaagca ggactcacag aacaggaacg caaactcctc
      241 cacgtactgg caacagcgga aaaaaacgac ttacaggcac aggagagcga acgaaaacag
      301 gcggtccaaa aacgaatcga gggaaaaaaa caacgacgag aacgcaatca ccgactcttt
      361 ctcgcggctg ggctactgat cgaagcagga ctggtagaca caaaaacagg cgagctatgc
      421 tataaaaaag acaggatatt acaggcactt aaggaaatta agtacgatct ggagacatcc
      481 ccaaacccag acgcgtaagt gcctccatcc gtgttccggt tccctggtgc ttcctcgctc
      541 attcgctcgc tacgctcggt catgagactg cggcgagcac gaccacctca atcatgcggt
      601 aagccgcacc attgctgggc tgagaggaga aaaccgccgg aaagcccgct gctcaaaaag
      661 acgccgaaag gcgctgttat ctgatatagg cttgttcatg tccgcgaatt taacccccca
      721 ttaacaaaaa acgggggtag tgttacttct ttgttaacta acatttaatt atttgtttct
      781 tggttagcca ttctccagaa ttatccatcc agcgtcgaat agtccggctg ctaacaccaa
      841 ccgccactgc aatatcttcc gttgacgctc ccaagatata catatcaagc gccctacgac
      901 gtttgtcgtc gttagcagtc caccgaacag cggcgctttt tttccctttg tccgactgat
      961 tttctgacga attggccttc ccgcccttgc gaccgcgtgc tgcctgaatt tctggcgtgt
     1021 gcgtatcagc cacatactgt gcgaaagttt ccggcgtgaa gttcctgtgc gtgtatttcg
     1081 caatgctctt gccaatagcc cgacattcag ccagtgaaag cggaacggga agcgatgcat
     1141 tgtacatttc gacacgctgg atcaccgctt caagccactg tgagaacgct ggccagccct
     1201 gacgaatcgc cctgtaagcc catttgcgcg tcatttcgaa caggtggcag tttcgcccca
     1261 tcccgtaatg tttatcgatg ctacgacgct ctgaggcgct caaatcgaga taatctgcca
     1321 gttcatcgag ggtataggcg tcctcgcgcc actccatcac ctgccattcc aggtggaacg
     1381 gatttttgca aatcaggccg ctgtagttca catcagcaca aagtttctca cacagcgaac
     1441 gttcaaccgc tgcggcatat ttcagcgcct taaccgaggc atcaggcgcg gttctcacgg
     1501 cgatgttgag tgcgtagagc aggtgagcgt gtccgttcac aggattttta acggtgatgt
     1561 tcggcgcggg ggcgttccgg tcgctccagt caatcgcagc cccctcgcgg tcaacgtcaa
     1621 aaaccagcca gaactgcgca tgaggctggt tctgctggat gtaccgcgca agaagcgcac
     1681 gccctttgcc ggagatgcga aggccgaaag cgagatcatc cgtgtgatag gggcggtggg
     1741 gtaaattttc ttcgaagtat tgaagcgcgg cgctcatgtg ttacgattcc ttccaggtta
     1801 tcgaccgacc tcgcccctgt attctcgtga caatcttggc ggagagacac gaatttcagg
     1861 ggcgtttgtt tttcagtcgc ttacactacc cccaacaaca aaacctgtcg agccttcccg
     1921 caaaaccgat ccatttacca taactcccgt tgtacgcccc cttaaaacgc cctcagtcgc
     1981 tctctggcgc aaaaaacgca aaaagacaag gaaacaccag gctaaaccag aaaaatgcgt
     2041 cagaatcgtt tttagcgcgt tgcataacta tgcacgaaag cgatgcgcga tctgtttcga
     2101 gcgttcagaa gggcgaacgg gtcaaaacag caaactttct catcagaaaa cggtgaacgg
     2161 gacgcggaat tttttcgcgg gtcgtgaggc gttggacaag cgaagcgcgt cagtttttcc
     2221 ggctcttgcc cgtgacaggt ttctccgcca gtttatcttc cagtgtcaca actttctgat
     2281 acaccgccgc tgtggcgttg tagttcctgt cgagcattgt tttcattccc catccaagca
     2341 cacagaacat aaccagaaaa gccactgaca ccccacccag ccatttccag ctataccctt
     2401 taagggtgtt gtattcctgc acgatattgc tgtgaattgt cgcaatatcc ctgttcaggg
     2461 catccgcgtt tgccttcatg tttgcgactg actcttccag ccgctgaaaa tcctggctga
     2521 tgcgctcacc tatcagccct gcaacatcca gcttctgcac ctcgtttctg acttcatccc
     2581 tgacctgttt tgccacaccg tcagaaatat cccgatatcc gcgaagtgtt tcccttgcca
     2641 cagccagaga atcagcaaca gctttctgtt gctccattgc ggtatgttgc agatgctcca
     2701 ccgataacag gagcgtgagt aatttttctt ctgtgctggc catgttcaga atcccataga
     2761 aaatccacgt gacggtgatt taacccgttc aggttcagtt cggttctgtc tgctcactct
     2821 gtctctcatg tcaaagccat gctcccgcgc aacatcatgt tgcagccttc tgaccagttc
     2881 atgttgctta accggagtgt ccagccattc cctgatgtca tacccgaccg ttcgcgcctg
     2941 ttcaagatgg cgggaatagt ccggttcaga ccgtttttgc atgatgtcat gacgctgggc
     3001 atcatcaagc cgtccggcag cttcaaaacc cagatgcact tcgggacgtc gttcaatgcc
     3061 ctgttctttc agcgtccggc agtcaatgaa gcccctttca aagccatgct ttctcatatg
     3121 ttcgttgtgc ttcacctccc agcgttttcg caattcccgc aactgctctt tttgctgagt
     3181 gagagtcagg cttccggaat cctttttcgc acctccccgc tcgggatacc tggcgttata
     3241 gcgccggaaa tactgttccg gtgtacgttc aatgccatca ttcacacgct ggctcatcat
     3301 gatatgcgca tgaggctgtt cgccgccgtc aatgctcgct ttcggattgt gaattgcaaa
     3361 actccaggcg tgccgttcgc cagcttcctg acgtacaaaa tcctgcacca gttcaaggcg
     3421 ctgttccgct gtcagttcac ggggtaatgc aatttcaagt tcccgatagg tcgaaccgtt
     3481 cgcacgttca aactggtcag cagcctgcca gaaatgtgag ggattatctc gcgcccattc
     3541 cggcatgttt ccgtgtgcgg aatattccaa atcctgacgg tcgcggtatt tctctttgcg
     3601 ctcgatgtaa tcggcgtggt ttgcagcctg ccccttgcca ccaaatttaa cgctgaggtg
     3661 ataggttgcc acggtttcag ccctccgcag gagcgcactg tttctcgacg aaggagagaa
     3721 acatataagt gcgcttcctt ctaatttta
//
