LOCUS       CP054322                5164 bp    DNA     circular BCT 10-JUN-2020
DEFINITION  Escherichia coli strain SCU-390 plasmid pSCU-390-3, complete
            sequence.
ACCESSION   CP054322
VERSION     CP054322.1
DBLINK      BioProject: PRJNA624897
            BioSample: SAMN14609796
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5164)
  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  JOURNAL   Unpublished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 5164)
  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                   :: 13x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 05/26/2020 18:17:01
            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)                     :: 5,020
            CDSs (total)                      :: 4,901
            Genes (coding)                    :: 3,691
            CDSs (with protein)               :: 3,691
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 1,210
            CDSs (without protein)            :: 1,210
            Pseudo Genes (ambiguous residues) :: 0 of 1,210
            Pseudo Genes (frameshifted)       :: 1,101 of 1,210
            Pseudo Genes (incomplete)         :: 108 of 1,210
            Pseudo Genes (internal stop)      :: 59 of 1,210
            Pseudo Genes (multiple problems)  :: 54 of 1,210
            ##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..5164
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-390"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-390-3"
                     /geo_loc_name="USA: California"
                     /collection_date="2018"
     gene            1456..2370
                     /locus_tag="HHJ49_25055"
     CDS             1456..2370
                     /locus_tag="HHJ49_25055"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001738986.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid replication protein"
                     /protein_id="QKN36149.1"
                     /translation="MSAALQYFEENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWLVMEWREEAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLEAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGSKSKRSTVATSARTL
                     KPWEALGISRAWYYQLKKRGLVE"
                     /name="plasmid replication protein"
     gene            complement(2574..3092)
                     /locus_tag="HHJ49_25060"
     CDS             complement(2574..3092)
                     /locus_tag="HHJ49_25060"
                     /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="QKN36150.1"
                     /translation="MRFLLILRISTEDTPCTRRPQAIYCTTTTHRKKTPGSITNMRISN
                     IEWLKKRIGFIRKLGEQTARQRQIIDLIDNEAGLTEQERKLLHVLATAEKNDLQAQESE
                     RKQAVQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTGELCYKKDRILQALKELKYD
                     LETSPNPDA"
                     /name="hypothetical protein"
     gene            3149..4075
                     /locus_tag="HHJ49_25065"
     CDS             3149..4075
                     /locus_tag="HHJ49_25065"
                     /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="QKN36151.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTPEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIDGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     LTQQKEQLRELRKRWEVKHNEHMRKHGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIREWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQDRTEPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            4078..4611
                     /locus_tag="HHJ49_25070"
     CDS             4078..4611
                     /locus_tag="HHJ49_25070"
                     /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="QKN36152.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQKLDVAGLIGERISHDFQRLEESVANMKVNADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFCVLGWGMKTILDRNYNATAAVYQKVVTLED
                     KLVEKPVTGKSRKN"
                     /name="hypothetical protein"
     gene            complement(4677..4886)
                     /locus_tag="HHJ49_25075"
     CDS             complement(4677..4886)
                     /locus_tag="HHJ49_25075"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_019842149.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QKN36153.1"
                     /translation="MAKLGENTPHIIDATVDFMASSQAFREYLKKLPPDNTIPPALTDE
                     HVPLYIRRLEYYRLLYRPKQTESY"
                     /name="hypothetical protein"
     Typing          1457..2370
                     /name="rep_cluster_2131"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.909"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3150..4072
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.701"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tggttgttgt tcttgttctg tatgtatata aacactatcg acatattatg accgggaaca
       61 ttccttaccc cctctgcgct cgcagaggtt ttttttgcca ttaattaata atgaactgaa
      121 atgcagttcc gatacctcca tttgcacatt atccctgaca tatggtaccg gaaccgcatt
      181 aattttatgt tataagagtt tatttttaat gtccagatgg tttaatagta tttatatgta
      241 attagctgta tggatagtac tggttttatt gtataacttg tcgttttttt ttattgtttt
      301 tgtgtggtgt gctaatcttt aagttataaa aaaacccctt ggaatacagg ggcaaaagta
      361 aggaaaacaa atggatgctc agtttgtgtg acactttaaa ctaatggaac tatagagtgg
      421 aggttgttac agtcgctttt ataaaacagc aaccagtttt tttcaatagt ctgatgatgg
      481 ttgtgacagt tttgtgatat tgttcaaaat gttttttgtt gaatgtttgt tttttggtct
      541 attggtgtct ggttttattt tttctgctat tacatatcaa gaaatgtgat tggtgtagca
      601 agagtggaat gcgatgtgga taaactaatt ggttgtcgaa tctaatttac ttagaaaact
      661 acacttgttt ttgtgtatga atttagtgaa tttgtctgtc tatgtgtttt cgtgcattta
      721 taaatccttc gtcaggatct taaatttagt gttgaatatg tagggcctgt acggtaatta
      781 ttatttagcg tagctacttc atcgttgttc gaacacaacc aacaacctgt aattgttgtt
      841 tctcttggtt ccccactttt gtggggtttt ttatctcttc cgtgcatcgt aaagcgcgga
      901 ctccttctgg aaaggttgtt ttagggcatc actgaggcat tttttgcgtt tgtgaatatt
      961 gagcatccga taactaaaat atttcccata gactctgatt cttgccaccg accccaggtc
     1021 ggtttttttt gtcctggcga gatgtgaagt ttggaaacag gaaaccccgt cagagcgcca
     1081 cgcaccaggg gagaaaactt gtcgttttga gccgttcggt gttcagaacg cacgaaaccg
     1141 atcgcacatc gctttcgtgc atagttatgc aacgccctga aaacgattct gacgcgtttt
     1201 tctggtttag cctggtgttt tcttgtcttt ttgcgttttt tgcgccagaa agcgattgag
     1261 ggcgttttac agggtacgta caacgggagt tatggtaaat ggatcggatt tgcgggaagg
     1321 ctcgacaggt tttgtcgttg ggggtagtgt aagcgactga aaaacaaacg cccctgaaat
     1381 tcgtgtctat ccgccaagac tttcacgaaa atacaggggc gatgtcggtc gataacctgg
     1441 aaggaatcgt aacacatgag cgccgcgctt caatacttcg aagaaaattt accccaccgt
     1501 ccctatcaca cggatgatct cgctttcggc cttcgtatct ccggcaaagg gcgcgcgctt
     1561 cttgcacggt atatccagca gaaccagcct catgcacagt tctggctggt ttttgacgtt
     1621 gaccgcgagg gggctgcgat tgactggagc gaccggaacg ctcccgcgcc gaacatcacc
     1681 gttaaaaatc ctgtgaacgg acacgctcac ctgctctacg cactcaacat cgccgtgaga
     1741 accgcgcctg atgcctcggt taaggcgctg aaatatgccg cagcggttga acgttcgctg
     1801 tgtgagaaac tttgtgcgga tgtgaactac agcggcctga tttgcaaaaa tccgttccac
     1861 ctggaatggc tggtgatgga gtggcgcgag gaagcctata ccctcgatga actggctgat
     1921 tatctcgatt tgagcgcctc agagcgtcgt agcatcgata aacattacgg gatggggcga
     1981 aactgccacc tgttcgaaat gacgcgcaaa tgggcttaca gggcgattcg tcagggctgg
     2041 ccagcgttct cacagtggct tgaagcggtg atccagcgtg tcgaaatgta caatgcatcg
     2101 cttcccgttc cgctttcact ggctgaatgt cgggctattg gcaagagcat tgcgaaatac
     2161 acgcacagga acttcacgcc ggaaactttc gcacagtatg tggctgatac gcacacgcca
     2221 gaaattcagg ctgcacgcgg tcgcaagggc ggttctaagt ctaagcgcag cacagtagct
     2281 acatctgcac gcacgctgaa accgtgggag gcattaggga tcagtcgcgc ctggtattac
     2341 caactgaaaa aacgaggtct cgtagagtag accaaataag cctatatcag ataacagcgc
     2401 ctttctggcg tctttttgag cagcaggttt tttgccgttt tcccccgttc agccctgcaa
     2461 tggcgcggct ttccgcgtga ttgtggtggt agtgctcgcc gcagtctcat gaccgagcgt
     2521 agcgagcgaa tgagcgagga agcaccaggg aatcggaaca cggatggagg cacttacgcg
     2581 tctgggtttg gggatgtctc cagatcgtac ttaagttcct taagtgcttg taatatcctg
     2641 tcttttttat agcatagctc gcctgttttt gtgtctacca gtcctgcttc gatcagtagc
     2701 ccagccgcga gaaagagccg gtgattgcgt tcccgtcgtt gtttttttcc ctcgattcgt
     2761 ttttggaccg cctgttttcg ttcgctctcc tgtgcctgta agtcgttttt ttccgctgtt
     2821 gccagtacgt ggagaagttt gcgttcctgt tctgtgagtc cggcttcgtt gtcgatcagg
     2881 tcaataatct gtctctgtcg tgcggtctgt tctccgagct tcctaatgaa tccgatccgt
     2941 ttcttcagcc attcgatgtt gctgatgcgc atgttcgtga tgctccctgg tgtttttttg
     3001 cggtgtgttg tggtcgtgca gtatatcgct tgcggtcggc gggtgcaggg ggtatcttcc
     3061 gtgctaattc gtaaaattag aaggaagcgc acttatatgt ttctctcctt cgtcgagaaa
     3121 cagtgcgctc ctgcagaggg ctgaaaccgt ggcaacctat cacctcagcg ttaaatttgg
     3181 tggcaagggg caggctgcaa accacgccga ttacatcgag cgcaaagaga aataccgcga
     3241 ccgtcaggat ttggaatatt ccgcacacgg aaacatgccg gaatgggcca gggataatcc
     3301 ttcccatttc tggcaggcgg ctgaccagtt tgaacgtgcg aacggttcga cctataggga
     3361 acttgaaatt gcattacccc gtgaactgac accggaacag cgccttgaac tggtgcagga
     3421 ttttgtacgt caggaagctg gcgaacggca cgcctggagt tttgccattc acaatccgaa
     3481 agcgagcatt gacggcggcg aacagcctca tgcgcatatc atgatgagtc agcgtgtgaa
     3541 tgatggcatt gaacgtacac cggaacagta tttccggcgc tataacgcca ggtatcccga
     3601 gcggggaggt gcgaaaaagg attccggaag cctgactctc actcagcaaa aagagcagtt
     3661 gcgggaattg cgaaaacgct gggaggtgaa gcacaacgaa catatgagaa agcatggctt
     3721 tgaaaggggc ttcattgact gccggacgct gaaagaacag ggcattgaac gacgtcccga
     3781 agtgcatctg ggttttgaag ctgccggacg gcttgatgat gcccagcgtc atgacatcat
     3841 gcaaaaacgg tctgaaccgg actattcccg ccatcttgaa caggcgcgaa cggtcgggca
     3901 tgacatcagg gaatggctgg acactccggt taagcaacat gaactggtca gaaggcttca
     3961 acatgatgtt gcgcgggagc atggctttga catgagagac agagtgagca gacaggaccg
     4021 aactgaacct gaacgggtta aatcaccgtc acgtggattt tctatgggat tctgaacatg
     4081 gccagcacag aagaaaaatt actcacgctc ctgttatcgg tggagcatct gcaacatacc
     4141 gcaatggagc aacagaaagc tgttgctgat tctctggctg tggcaaggga aacacttcgc
     4201 ggatatcggg atatttctga cggtgtggca aaacaggtca gggatgaagt cagaaacgag
     4261 gtgcagaagc tggacgtagc agggctgata ggtgagcgca tcagccatga ttttcagcgg
     4321 ctggaagagt cagtcgcaaa catgaaggta aacgcggatg ccctgaacag ggatattgcg
     4381 acaattcaca gcaatatcgt gcaggaatac aacaccctta aagggtatag ctggaaatgg
     4441 ctgggtgggg tgtcagtggc ttttctggtt atgttctgtg tgctcggatg gggaatgaaa
     4501 acaatactcg acaggaacta caacgccaca gcggcggtgt atcagaaagt tgtgacactg
     4561 gaagataaac tggtggagaa acctgtcacg gggaagagcc ggaaaaactg acgcgcttcg
     4621 cttgtccaac gcctcacgac ccgcgaaagg atttcgcgaa ccgttcaccg tttttttcaa
     4681 tatgattctg tctgctttgg tcgataaagc agacgatagt attccagcct tcgtatatat
     4741 aacggtacgt gctcatcagt aagagctggc ggtattgtgt tatcaggggg aagttttttc
     4801 agatactcac gaaatgcctg gcttgatgcc ataaaatcta cagtagcatc gataatatgt
     4861 ggggtgtttt cacctaattt tgccatgatg ataatcctta tattatcacg gtttgtgaat
     4921 gatagggtgt cactattatt tatgcgttag tgaaccagaa aaaatccccc gttggcatag
     4981 ggggatatgt aaggagaaat aacttcgcag gtgttcttgt ttgtataacg tgaaaagact
     5041 gcacgcaact taataagtct gccgtactta ctttcagttt tcaacataag gtttataaca
     5101 atgtatggaa tggaagtgag ctttaaggtt tcagctctaa aaaataaaat atttattagt
     5161 tggc
//
