LOCUS       NZ_CP051703             5391 bp    DNA     linear   CON 02-MAY-2020
DEFINITION  Escherichia coli strain SCU-125 plasmid pSCU-125-3, complete
            sequence.
ACCESSION   NZ_CP051703
VERSION     NZ_CP051703.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14609785
            Assembly: GCF_012934655.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5391)
  AUTHORS   Stephens,C., Arismendi,T., Wright,M., Gonzalez,A., Gill,M.,
            Hartman,A., Pandori,M. and Hess,D.
  TITLE     F plasmids are the primary drivers of antibiotic resistance in
            human-associated commensal E. coli
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5391)
  AUTHORS   Stephens,C., Arismendi,T., Wright,M., Gonzalez,A., Gill,M.,
            Hartman,A., Pandori,M. and Hess,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-APR-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                   :: 14x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 05/01/2020 12:31:40
            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)                     :: 5,196
            CDSs (total)                      :: 5,069
            Genes (coding)                    :: 4,913
            CDSs (with protein)               :: 4,913
            Genes (RNA)                       :: 127
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 99
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 156
            CDSs (without protein)            :: 156
            Pseudo Genes (ambiguous residues) :: 0 of 156
            Pseudo Genes (frameshifted)       :: 67 of 156
            Pseudo Genes (incomplete)         :: 77 of 156
            Pseudo Genes (internal stop)      :: 46 of 156
            Pseudo Genes (multiple problems)  :: 29 of 156
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence was derived from
            CP051703.
            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..5391
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-125"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-125-3"
                     /geo_loc_name="USA: California"
                     /collection_date="2016"
     gene            complement(<1..276)
                     /gene="psiB"
                     /locus_tag="HHJ38_RS25885"
                     /old_locus_tag="HHJ38_25920"
     CDS             complement(<1..276)
                     /gene="psiB"
                     /locus_tag="HHJ38_RS25885"
                     /old_locus_tag="HHJ38_25920"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052658.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="conjugation system SOS inhibitor PsiB"
                     /protein_id="WP_042101177.1"
                     /translation="MKTELTLNVLHTMNAQEYEDIRAAGSDERRELTHAVMRELDAPDN
                     WTMNGEYGSEFGGFFPVQVRFTPAHERFHLALCSPGDVSQVWVLVLV"
                     /name="psiB"
     gene            complement(331..2289)
                     /locus_tag="HHJ38_RS25890"
                     /old_locus_tag="HHJ38_25925"
     CDS             complement(331..2289)
                     /locus_tag="HHJ38_RS25890"
                     /old_locus_tag="HHJ38_25925"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052657.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ParB/RepB/Spo0J family partition protein"
                     /protein_id="WP_169063644.1"
                     /translation="MPVTKCEPETTRKASRKXXKTQETXLSALLAQTEEVSVPLXSLIK
                     SPLNVRTVPYSAESVSELAXSIKGVGLLQNLVVHXLPGDRYGVAAGGRRLAALNMLAER
                     XIJPADWPVRVKVIPQELATAASMTENGXRRDMHPAEQIAGFRAMAQEGKTPAQIGDLL
                     GYSPRHVQRMLKLADLAPVILDALAEDRITTEHCQALALENDTARQVQVFEAACQSGWG
                     GKPDVRVIRNLITESEVAVAGNSKFRFVGADAFSPDELRTDLFSDDXXGYVDXVALDAA
                     LLEKLQAVAEXLREAEGWEWCAGRMEPVGECREDAGTYRCLPEPEAVLTEAEEERLNEL
                     MARYDALENQCEESDLLEAEMKLMRCMAKVRAWTPEMRAGGGVVVSWRYGNVCVQRGVQ
                     LRSEDDAADDADRTEQVQEKASVEEISLPLLTKMSSERTLAVQAALMQQPDKSLTLLAW
                     TLCLNVFGSGAYSKPAQISLECKHYSLTSDAPSGKEGAAFMALMAEKARLAALLPEGWS
                     RDMTTFLSLSQEVLLSLLSFCTACSLNGVQTREYGHTSRSPLDTLESAIGFHMRDWWQP
                     TKANFFGHLKKPQIIAALNEAGLSGAARDAEKMKKGDAAEHAEHHMKDNRWVPGWMCAP
                     RPQTDATERTDNLADAA"
                     /name="ParB/RepB/Spo0J family partition protein"
     gene            complement(2348..2581)
                     /locus_tag="HHJ38_RS25895"
                     /old_locus_tag="HHJ38_25930"
     CDS             complement(2348..2581)
                     /locus_tag="HHJ38_RS25895"
                     /old_locus_tag="HHJ38_25930"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_958724.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF905 family protein"
                     /protein_id="WP_169063645.1"
                     /translation="MSEYFRILQGLPDGSFTREQAEAVAAQYRNVFIEDDQGTHFRLVV
                     RXBXXLXWRXWNFEDGAGYWMNXXIRBFGILK"
                     /name="DUF905 family protein"
     gene            complement(2639..3166)
                     /locus_tag="HHJ38_RS25900"
                     /old_locus_tag="HHJ38_25935"
     CDS             complement(2639..3166)
                     /locus_tag="HHJ38_RS25900"
                     /old_locus_tag="HHJ38_25935"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052656.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="single-stranded DNA-binding protein"
                     /protein_id="WP_169063646.1"
                     /translation="MAVRGINKVILVGRLGKDQEVRYIPNGGAVANLQVATSETWRDKQ
                     TGEMKEQTEWHRVVLFGKLAEVAGEYLRKGAQVYIEGQLRTRSWEDNGITRYVTEILVK
                     TTGTMQMLGSAPQQNAQVQPQPQQNGQPQSADATKKGSAKTKGRGRKAAQPEPQPQPPE
                     GEDYXFSDDIPF"
                     /name="single-stranded DNA-binding protein"
     gene            3231..3467
                     /locus_tag="HHJ38_RS25905"
                     /old_locus_tag="HHJ38_25940"
     CDS             3231..3467
                     /locus_tag="HHJ38_RS25905"
                     /old_locus_tag="HHJ38_25940"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001404411.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001337416.1"
                     /translation="MTFCGDLPFVPSGIHHHLFENLRRKGHHCHGLTHLSWAERKIFYR
                     VLGKKFCGLFIYPGQSVRQVVAVSAPGDRGLNR"
                     /name="hypothetical protein"
     gene            3468..3846
                     /locus_tag="HHJ38_RS25910"
                     /old_locus_tag="HHJ38_25945"
                     /pseudo=""
     CDS             3468..3846
                     /locus_tag="HHJ38_RS25910"
                     /old_locus_tag="HHJ38_25945"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001451816.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     gene            complement(4083..4241)
                     /locus_tag="HHJ38_RS25915"
                     /old_locus_tag="HHJ38_25950"
     CDS             complement(4083..4241)
                     /locus_tag="HHJ38_RS25915"
                     /old_locus_tag="HHJ38_25950"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052660.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type I toxin-antitoxin system Hok family toxin"
                     /protein_id="WP_001302184.1"
                     /translation="MKLPRSSLVWCVLIVCLTLLIFTYLTRKSLCEIRYRDGYREVAAF
                     MAYESGK"
                     /name="type I toxin-antitoxin system Hok family toxin"
     gene            complement(4517..5236)
                     /locus_tag="HHJ38_RS25920"
                     /old_locus_tag="HHJ38_25955"
     CDS             complement(4517..5236)
                     /locus_tag="HHJ38_RS25920"
                     /old_locus_tag="HHJ38_25955"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016233040.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid SOS inhibition protein A"
                     /protein_id="WP_001276230.1"
                     /translation="MSARSQALVPLSTEQQAAWRAVAETEKRRHQGNTLAEYPYAGAFF
                     RCLNGSRRISLSDLRFFMPSLTAEELHGNRLQWLYAIDVLIETQGEVCLLPLPGDAAER
                     LFPSVRFCVRERSRHKSALVMQKYSRQQAREAEQKARAYQALVAQAEIELAFHSPETVG
                     SWHARWSDRVAEHDLETLFWQWGERFPSLAGMERWQWQDMPFWQVIAEASLAAKEAGHA
                     VREMERWMVPNKLREVA"
                     /name="plasmid SOS inhibition protein A"
     gene            complement(5233..>5391)
                     /gene="psiB"
                     /locus_tag="HHJ38_RS25925"
                     /old_locus_tag="HHJ38_25960"
                     /pseudo=""
     CDS             complement(5233..>5391)
                     /gene="psiB"
                     /locus_tag="HHJ38_RS25925"
                     /old_locus_tag="HHJ38_25960"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052658.1"
                     /note="incomplete; too short partial abutting assembly gap;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="conjugation system SOS inhibitor PsiB"
                     /name="psiB"
ORIGIN
        1 caccagaacc agcacccaga cctgggagac atcgcccggt gaacataacg ccaggtgaaa
       61 acgttcgtgg gcaggcgtga aacggacctg gacggggaaa aagccgccaa actcgctgcc
      121 gtactcgccg ttcatcgtcc agttgtccgg cgcatccagt tcccgcatca cggcgtgtgt
      181 cagctcacga cgttcatcac ttccggcagc ccggatatct tcatattcct gtgcgttcat
      241 ggtatgtaat acattcagag tcagttcagt tttcatcacg gtatctccct tgctgccgcc
      301 ccgtctccgg cggggcgatg tggttgttca tcaggcggca tcagccaggt tatcggtgcg
      361 ttcagtggca tccgtctgtg ggcgtggtgc acacatccag ccaggcaccc agcggttgtc
      421 tttcatatgg tgctctgcat gttcagccgc atcgcctttc ttcatcttct ccgcgtcccg
      481 tgcggcaccg gatagtcctg cctcattcag ggctgcgata atctgcggct ttttcaggtg
      541 tccgaaaaag tttgctttcg tcggctgcca ccagtcgcgc atgtgaaagc cgatggcgct
      601 ctccagcgtg tccagcggac tgcgtgacgt gtgaccatac tcacgggtct ggacaccgtt
      661 aaggctgcat gcggtgcaga aactgagcag ggataacagc acctcctgac tgagtgacag
      721 gaatgtcgtc atgtcccgtg accatccctc cggtaacagg gcagcaagac gggctttttc
      781 tgccatcagc gccatgaatg cggcaccttc cttccccgat ggcgcatcgc tggtcagcga
      841 ataatgttta cattccaggc tgatttgtgc tggtttactg tacgctccgc tgccaaacac
      901 attcaggcag agcgtccatg ccagcagtgt cagggatttg tccggttgct gcatcagtgc
      961 tgcctggact gccagcgtgc gttcggaaga cattttcgtc agcagtggca gactgatttc
     1021 ctccactgac gctttttcct gcacctgttc cgtgcggtca gcgtcgtcag ccgcatcatc
     1081 ctcactgcgt aactgcacac cacgctggac acatacgttt ccataacgcc aggacaccac
     1141 cactccacct ccggcacgca tctccggcgt ccacgctctg accttcgcca tgcagcgcat
     1201 cagcttcatt tctgcttcca gcaggtcaga ttcctcacac tggttttcca gcgcgtcgta
     1261 acgtgccatc agttcgttca gacgttcttc ttccgcctcg gtcagcaccg cttccggctc
     1321 cggcagacag cggtatgttc cggcatcctc acggcactca ccgacaggct ccatgcgtcc
     1381 ggcgcaccat tcccagcctt cggcttcccg aaggwrytcw gcgacagcct ggagtttttc
     1441 cagcagggcr gcatcgagcg ccacgcrgtc sacatarccr yccycgtcrt cgctgaacaa
     1501 atcrgtgcgc agttcgtctg gcgagaargc atcagccccc acgaagcgga atttactgtt
     1561 ccccgccacc gccacttcac tttccgtaat cagattgcgg ataacccgca catccggttt
     1621 tccgccccat cccgactgac aggcrgcttc aaacacctgy acctgacgcg cggtgtcgtt
     1681 ctccagcgcc agcgcctgac agtgytcggt ggtgatgcgg tcttctgcca gcgcatcgag
     1741 gatracmggm gcaaggtcag ccagtttcag cattcgctga acgtggcggg gtgaatagcc
     1801 cagcaaatca ccgatttgtg caggtgtttt gccttcctgc gccattgcgc ggaatccggc
     1861 aatctgttcr gcagggtgca tatcccgacg mtgaccgtty tcrgtcatyg atgcsgcmgt
     1921 cgccagctcc tgcggaatga ccttcacrcg kacaggccag tcagccggaa kgatgyyrcg
     1981 ctctgccagc atgttgagtg cwgccagtcg gcgaccrcct gcggcgacac cgtaacggtc
     2041 accwggcagr gyatgmacra ccagattctg carcaggccr ackcccttaa tggamtcagc
     2101 cagttcrctg acggactccg cagaatacgg caccgtgcgc acattcagcg gtgatttaat
     2161 cagtgarkcc agcggcacrc tcacttcctc cgtctgcgcc agcagggcag acagkrcwgt
     2221 ttcctgcgtt tttrcakatt tacggcttgc tttgcgggtg gtttctggtt cacacttcgt
     2281 tacaggcata atcatcccct tataattgct tatgtcctgc cggacgttyg cgcgtccggc
     2341 acctctctta cttaagaats ccgaaatycc kgatgwmmyg gttcatccag tacccggcac
     2401 cgtcctcaaa attccaggwg cgccagayca rssyrcyrty mtkrcggaca accaggcgaa
     2461 aatgcgttcc ctgatcatcc tcgataaaga crttccggta ctgtgcggca acggcttcmg
     2521 cctgttcgcg ggtaaaggag ccgtcmggca gyccctgaag tattctgaaa tattcgctca
     2581 tcctcatmtc tccggtgatg ccccgcacwg grcggggcgg ttktcacagt cagycmkatc
     2641 agaacgggat atcgtctgaa aaccmgtaat cctcmccctc cggcggttgc ggctgaggct
     2701 cyggctgcgc agccttacgt ccacggcctt tcgttttcgc gctccctttt ttcgttgcgt
     2761 cagcactctg tggctggccg ttctgctgag gctgcggttg cacctgagcg ttctgctgtg
     2821 gtgcactccc cagcatctgc atggtgcccg tggttttcac aaggatttca gtgacgtaac
     2881 gggtaatacc gttatcttcc cagctacggg tacggagttg cccctcgatg tagacctgcg
     2941 cgcccttacg cagatattca cctgccactt ccgcgagctt gccgaacagc accacgcggt
     3001 gccattccgt ctgttccttc atttcccccg tctgtttgtc gcgccaggtt tctgacgtgg
     3061 cgacctgcag gtttgccact gcgcccccgt tggggatgta acggacttcc tgatcttttc
     3121 ccagacgacc gacaagaatg accttgttaa ttccacgaac tgccatgatg tgtctccttc
     3181 tgttgatgtt ttcagccccc atcatctgtt gagtttcggg agccgcggtt ttgacgtttt
     3241 gcggggacct gccttttgtt ccctccggta ttcaccatca cctgtttgag aaccttcgcc
     3301 gcaaggggca tcactgccac ggcctgacgc acctgtcctg ggcagaacgc aaaatttttt
     3361 accgggtttt gggtaaaaaa ttttgtgggc tgttcattta ccctggacag tcagtgcggc
     3421 aggttgtggc tgtatcagcc cccggcgaca ggggcttaaa caggtgaatg gcaccggaca
     3481 caacaacggg cagggacccg ccgcaacgac gkrragcgcg kkytgcgaaa cggcgttgcg
     3541 ccttacatcc cggcgkcstt ttgccgggat gccaggagcg caggccacgg cgcgacagag
     3601 gcggcgcgac cggaacggtc gctgcaagcc cggggtttcg cgtcagggat ggaagcccgc
     3661 cagggcggag acagcttcgc tggctccgtt cacgacagcc cgccccgcca gggggacgcc
     3721 cggaaaaggc ataagcagga gaacaacaaa acagacaata atcagggcag cagtaatcag
     3781 agtcagagca gtaatcagag tcagagcagg aggaaaaaga gaataatcaa agggaaggtg
     3841 atgtgatttc tggcaagtca taaacagaga aggcggggga aaagaacggg cgccgcaggc
     3901 gcacgttcat ccccgttccc ggagggaaac ggccttcctg gcagtctggt tgttcagccc
     3961 gtacaatgcc agcaaggaga aagggaccac cggcgaacca gcagcccctt tataaaggcg
     4021 cttcagtgca gtcagaccag catcagccct gaaaaggcgg gcctgcgccc gcctccaggt
     4081 tgctacttac cggattcgta agccatgaaa gccgccacct ccctgtatcc gtctctgtaa
     4141 cgaatctcgc acagcgattt tcgtgtcaga taagtgaata tcaacagtgt gagacacacg
     4201 atcaacacac accagacaag agagctgcgt ggtagtttca tggccttctt ctccttgcgc
     4261 aaagcgcggt aagaggctat cctgatgttg tctaagcatg caggggcctc gtgggttaat
     4321 gaaaaattaa ctacggggct tttgtccttc tgccacacaa cacggtaaca aaccaccttc
     4381 acgtcatgag gcagaaaacc tcaagcgccg ggcacatcat agcccatata ccagcacgct
     4441 gaccacattc acttttcctg aaaataactc gctcattcag gctgtttacg ggcaatccgt
     4501 tgtgattgtt gccgcatcac gccacctccc ggagtttgtt cggcaccatc caccgctcca
     4561 tctcacggac agcatgaccg gcctcctttg ctgccagact ggcttccgcg ataacctgcc
     4621 agaatggcat atcctgccac tgccagcgtt ccattccggc cagtgacgga aaacgctcgc
     4681 cccactgcca gaacagggtt tccaggtcat gctctgccac ccgatcactc cagcgtgcat
     4741 gccagcttcc gactgtttcc ggtgaatgga acgccagttc gatttcagcc tgggcgacca
     4801 gcgcctggta cgcacgggct ttctgctctg cctccctcgc ctgctggcgg ctgtacttct
     4861 gcatgaccag cgcggattta tggcgactgc gttccctgac acaaaaccgc accgacggga
     4921 acaagcgttc tgctgcatca ccgggaaggg gaaggaggca gacctcgccc tgtgtttcaa
     4981 tcagcacatc gatggcatac aaccactgaa gacggtttcc gtgcagttct tctgcggtca
     5041 gggatggcat gaaaaatcgc aggtcagaca gcgatatcct gcggcttccg ttcagacagc
     5101 ggaaaaacgc ccccgcatac ggatattccg ccagcgtgtt tccctgatgg cggcgttttt
     5161 ccgtctctgc cactgcccgc catgcggcct gttgctctgt gctgagggga accagtgcct
     5221 gtgaacgtgc gctcatacct gacctccttc cgccatcagg atatggatga tgtcgttaac
     5281 gctgtatccc tgcgtatcca gtgacgccgc cagtgccagt gaatggctga cggcttccgg
     5341 tgcaaaccgc cgctgtacct gaaccaccgc aaacggctca ccaccggcat t
//
