LOCUS       NZ_CP054358             5153 bp    DNA     circular CON 13-JUN-2023
DEFINITION  Escherichia coli strain SCU-172 plasmid pSCU-172-5, complete
            sequence.
ACCESSION   NZ_CP054358
VERSION     NZ_CP054358.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14943545
            Assembly: GCF_013315695.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5153)
  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  JOURNAL   Unpublished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 5153)
  AUTHORS   Stephens,C., Arismendi,T., Wright,M., Hartman,A., Gonzalez,A.,
            Gill,M., Pandori,M. and Hess,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (18-MAY-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                   :: 78x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/13/2023 03:55:40
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,461
            CDSs (total)                      :: 5,339
            Genes (coding)                    :: 5,056
            CDSs (with protein)               :: 5,056
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 94
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 283
            CDSs (without protein)            :: 283
            Pseudo Genes (ambiguous residues) :: 0 of 283
            Pseudo Genes (frameshifted)       :: 85 of 283
            Pseudo Genes (incomplete)         :: 198 of 283
            Pseudo Genes (internal stop)      :: 39 of 283
            Pseudo Genes (multiple problems)  :: 33 of 283
            Pseudo Genes (short protein)      :: 3 of 283
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP054358.1.
            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..5153
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-172"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-172-5"
                     /geo_loc_name="USA: California"
                     /collection_date="2017"
     gene            complement(join(5069..5153,1..53))
                     /locus_tag="HPE50_RS26890"
                     /old_locus_tag="HPE50_26890"
     CDS             complement(join(5069..5153,1..53))
                     /locus_tag="HPE50_RS26890"
                     /old_locus_tag="HPE50_26890"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001405930.1"
                     /GO_component="GO:0019867 - outer membrane [Evidence IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin release lysis protein"
                     /protein_id="WP_001329514.1"
                     /translation="MRKRFFVGIFAINLLVGCQANYIRDVQGGTVAPSSSSKLTGISVQ
                     "
                     /name="colicin release lysis protein"
     gene            215..442
                     /locus_tag="HPE50_RS26895"
                     /old_locus_tag="HPE50_26895"
     CDS             215..442
                     /locus_tag="HPE50_RS26895"
                     /old_locus_tag="HPE50_26895"
                     /inference="COORDINATES: protein motif:HMM:NF015489.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin E1 immunity protein"
                     /protein_id="WP_015056439.1"
                     /translation="MLYAIVISTILCPYSKYAIEHIFFKFIKKDFFRKRKNLNNAPVAK
                     LNLFMLYNLLCLVLAIPFGLLGLFISIKNN"
                     /name="colicin E1 immunity protein"
     gene            complement(439..2004)
                     /locus_tag="HPE50_RS26900"
                     /old_locus_tag="HPE50_26900"
     CDS             complement(439..2004)
                     /locus_tag="HPE50_RS26900"
                     /old_locus_tag="HPE50_26900"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000447006.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA];
                     GO:0050829 - defense response to Gram-negative bacterium
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin-like pore-forming protein"
                     /protein_id="WP_000447003.1"
                     /translation="METAVAYYKDGVPYDDKGQVIITLLNGNPDGSGSGGGGGTGGSKS
                     ESSAAIHATAKWSTAQLKKTQAEQAARAKAAAEAQAKAKANRDALTQHLKDIVNEALRH
                     NSTHPEVIDLAHANNAAMQAEAERLRLAKAEEKARKEAEAAEKAFQEAEQRRKEIEKEQ
                     AETERQLKLAEDEEKRLAALSEEARAVEVAQKNLAAAQSELAKVDEEINTLNTRLSSSI
                     HARDAETNTLSGKRNELDQASAKYKELDERVKLLSPRANDPLQSRPFFEATRLRARAGD
                     EMEEKQKQVTASETRLNQISSEINGIQEAISQANNKRSTAVSRIHDAEDNLKTAQTNLL
                     NSQIKDAVDATVSFYQTLSEKYGEKYSKMAQELADKSKGKKISNVNEALAAFEKYKDVL
                     NKKFSKADRDAIFNALEAVKYEDWAKHLDQFAKYLKITGHVSFGYDVVSDILKIKDTGD
                     WKPLFLTLEKKAVDAGVSYVVVLLFSVLAGTTLGIWGIAIVTGILCAFIDKNKLNTINE
                     VLGI"
                     /name="colicin-like pore-forming protein"
     gene            2264..2701
                     /locus_tag="HPE50_RS26905"
                     /old_locus_tag="HPE50_26905"
     CDS             2264..2701
                     /locus_tag="HPE50_RS26905"
                     /old_locus_tag="HPE50_26905"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001749514.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001318234.1"
                     /translation="MGHCNFMAWHTLRDALKMTGRSRSQFYRDMRSGLVSYRTSQDGRR
                     EFETSELIRAYGELKRNETPERHTQGHSEKPHDQQTERILRELNELKQCLTLMLEDKQA
                     QDTERRRQEAERKQLQNEIAQLRQALEQEKKRGFWSRLFGH"
                     /name="hypothetical protein"
     gene            2782..3201
                     /locus_tag="HPE50_RS26910"
                     /old_locus_tag="HPE50_26910"
     CDS             2782..3201
                     /locus_tag="HPE50_RS26910"
                     /old_locus_tag="HPE50_26910"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016247941.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Exc2 family lipoprotein"
                     /protein_id="WP_001254967.1"
                     /translation="MRRTGNKLCLIAMITATVALTACTPKGSVEQHTRHYVYASDDGFD
                     PNFSTQKADTTRMMVPFFRQFWDMGAKDKATGKSRSDVQQRIQQFHSQEFLNSLRGTTQ
                     FAGTDYRSKDLTPKKSRLLADTISAVYLDGYEGRQ"
                     /name="Exc2 family lipoprotein"
     gene            complement(3426..3749)
                     /gene="mobA"
                     /locus_tag="HPE50_RS26915"
                     /old_locus_tag="HPE50_26915"
     CDS             complement(3426..3749)
                     /gene="mobA"
                     /locus_tag="HPE50_RS26915"
                     /old_locus_tag="HPE50_26915"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_000166966.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            4033..4227
                     /locus_tag="HPE50_RS26920"
                     /old_locus_tag="HPE50_26920"
     CDS             4033..4227
                     /locus_tag="HPE50_RS26920"
                     /old_locus_tag="HPE50_26920"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041639.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_001041621.1"
                     /translation="MNKQQQAVLNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA
                     EELQNSIQTRFEVENSTER"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(4306..4467)
                     /locus_tag="HPE50_RS26925"
                     /old_locus_tag="HPE50_26925"
     CDS             complement(4306..4467)
                     /locus_tag="HPE50_RS26925"
                     /old_locus_tag="HPE50_26925"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002224432.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_023144195.1"
                     /translation="MEKRLRRWLLPVLCFLLTCSFRLYPLILWITVLPLLSELTPLAAV
                     ERPSVASQ"
                     /name="hypothetical protein"
     Typing          complement(3759..3998)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="7.6e-123"
     Typing          4257..4786
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.579"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          complement(3430..3749)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="3.11e-62"
ORIGIN
        1 catccaacaa ggaggtttat agcgaatatt cccacaaaaa atcttttcct cataactcga
       61 tccttataaa atgaaaagaa tatataacga ggtttaattt atgagtttaa gatactacat
      121 aaaaaatatt ttgtttggcc tatactgcgc acttatatat atatacctta taacaaaaaa
      181 caacgaaggg tattatttcc tagcgtcaga taagatgcta tacgcaatag tgataagcac
      241 tattctatgc ccatattcaa aatatgctat tgaacacata ttttttaagt tcataaagaa
      301 agattttttc agaaaaagaa aaaacctaaa taatgccccc gtggcaaaat taaacctatt
      361 tatgctatac aatctacttt gtttggtcct agcaatccca tttggattgc taggactgtt
      421 tatatcaata aagaataatt aaatacccaa cacctcattt atagtattaa gtttattctt
      481 atcaataaag gcacatagaa tgcctgtaac aatagcaatc ccccagatac ctaatgtagt
      541 tccagcaagc acactaaaaa gtaaaacaac aacataacta actccagcat ctacagcttt
      601 cttctctaat gtaagaaata gcggcttcca gtcacctgta tccttaattt ttaggatatc
      661 agataccaca tcatatccaa aagaaacatg tcccgtaatc ttcaagtact tggcaaactg
      721 atctaaatgc ttagcccagt cttcatactt aaccgcctcc agtgcattga aaattgcatc
      781 acggtctgct ttgctgaatt tcttatttaa tacatccttg tatttctcaa aagcagctag
      841 agcttcattc acattgctga ttttcttacc tttagattta tcagcaagtt cctgtgccat
      901 ttttgaatat ttttcaccat atttttcaga tagcgtttga taaaagctaa ctgttgcatc
      961 cacagcatcc ttaatctgcg agttcaggag attagtctgt gctgttttca aattatcttc
     1021 agcatcatga atacgtgaaa ctgctgtact tcgcttatta ttagcctgag aaatagcctc
     1081 ttggattcca tttatctcag agctaatctg gttaagacgc gtttctgatg ctgttacctg
     1141 cttttgtttt tcctccatct catcaccagc tctcgcccgt agtctggtgg cctcaaaaaa
     1201 aggacgactc tgaagcggat cattcgccct aggagataaa agtttaaccc tttcatccag
     1261 ttctttatat ttagcagatg cctgatccaa ctcatttcgt tttccggaca gcgtattcgt
     1321 ttctgcatca cgggcatgaa tactggagct taaacgggta ttgagcgtat taatctcttc
     1381 atccactttc gccagctcag attgtgcagc agcaagattt ttttgtgcca cctccacagc
     1441 ccgggcctct tcactcaatg ctgccaggcg tttctcttca tcctcagcca gtttcaattg
     1501 gcgttctgtt tcagcctgct ccttctctat ctctttacgt cgttgttctg cttcctgaaa
     1561 agccttttcc gcagcttccg cttctttacg ggctttttct tctgcttttg caaggcgcaa
     1621 ccgctctgct tctgcctgca tcgctgcatt attggcatga gccaggtcaa taacctccgg
     1681 atgagtggaa ttatggcgaa gcgcctcatt cacaatatcc ttcagatgtt gagtcagcgc
     1741 atcccggttt gctttcgctt tagcctgtgc ttctgcggca gcttttgctc gggcagcctg
     1801 ttctgcctgc gttttcttca attgagcagt agaccattta gctgtggcat gaatggctgc
     1861 agaactttca cttttgctac ctccagttcc accaccaccg ccagagccac tcccgtctgg
     1921 attaccattc aaaagagtaa tgattacctg ccccttatca tcataaggaa caccatcttt
     1981 atagtacgct acagctgttt ccattataaa atcctctttg acattaaaaa caaatagtta
     2041 aaagcaatat actgtatata taatcactgg ttttatatac agtttaaaat tacgccgctg
     2101 cattttccct gtcaaccctg tggattttca tttttgtgaa aacgatcaaa aaaacagcca
     2161 cccacaccac gtgctatttc cacccgatgc cacaaaaacc agcacaaaca ttaccgttct
     2221 cagacctcat tatgttttac tgaaaccatg agatgagaca cctatgggac actgtaactt
     2281 tatggcatgg cacacactcc gggacgcact gaaaatgact ggaagatcgc gttcacagtt
     2341 ttaccgtgat atgcgctcag gtcttgtcag ttaccgtacc agccaggacg gacgacggga
     2401 gtttgaaacc agtgaactga tccgggcata cggcgaatta aagcggaatg agacaccaga
     2461 aaggcacact caaggacact cagaaaaacc tcatgatcag cagacagaac gcattctccg
     2521 ggaactgaat gagctgaaac aatgcctgac gctgatgctt gaggataaac aagcccagga
     2581 tacggagcgc cggcgccagg aagcagaacg gaaacagcta cagaatgaga tagcccagct
     2641 caggcaggct ctggagcagg aaaagaaacg gggattctgg tccaggctgt tcggtcactg
     2701 aacgcgctca gaaactgatg ataagataat cttcggataa taactcaccg agaataaata
     2761 ctttaaggta gggagacact catgagacgt accggaaaca aactttgtct tatcgccatg
     2821 ataacagcaa cagtagctct cacagcctgt accccaaagg gcagcgtgga acaacatacc
     2881 cggcattacg tatatgcttc tgatgacggt tttgatccca acttttccac ccaaaaagcc
     2941 gacacaacac gaatgatggt gccttttttt cggcagttct gggatatggg agctaaagat
     3001 aaagcgacag gaaaatcacg gagtgatgtg caacaacgca ttcaacagtt tcacagccag
     3061 gaatttttaa actcactccg gggcacaact caatttgcgg gtactgatta ccgcagcaaa
     3121 gaccttaccc cgaaaaaatc caggctgctg gctgacacga tttctgcggt ttatctcgat
     3181 ggctacgagg gcagacagta agtggattta ccataatccc ttaattgtac gcaccactga
     3241 aacgcgctga acgcgattct gacgcagaca ccgcaaaaag agatgtttta ccccggaaaa
     3301 acaggaagga tgcgtcagga tcgttttcag ctctctgcat agctatgcat gaaagcgaat
     3361 ggtgatcact ttgggagctt acggtgttca taccgtcagt tttcgacagt tttctctccg
     3421 ggaagctaat ctgccataag cctggataac agggcacggt gatactccgt aatagcgatc
     3481 agcacctccg catactccct gtccccgaca cgcttgccgt cgataaagag ttttttctgt
     3541 aacgccccca gtctcataac ttctttcagt acccgatcat cagtcagtga gttaactttc
     3601 ttaccgagag ctgccgcccg taaaaaaccg gaaacggtct tgccgcattc agcagccctt
     3661 tttctgattt cctggtcttc ttctgccgtc agacgaacag ggcgactgat agcccgcctg
     3721 cgcgtattac ttccacttcg ttttgtcata aaacatggct ccgtatctga catgggtgtc
     3781 ggggcaaagc cctgaccagg gtaattgtaa tagcgtgcat gtatgcgcgg tataacaatt
     3841 acacatcctg tcctgtcagc aagttcgaat taccgacaaa ggcacggcag ttttttggca
     3901 gtgacagtat tgtcaggcag aaatacccgt caaagcgtca gacggcagaa taccggcggt
     3961 aaaacagtcg aaaagtggta cgcgatataa tcacacaacg cagatgacag acagaacgga
     4021 gaaaacgaaa agatgaacaa gcagcagcaa gccgtactca acatggcagg attcataaaa
     4081 agccaaagcc tgacgctgct cgaaaagctg gacgcactcg atgctgacga acaggctacc
     4141 atgtgtgaga agctgcacga actcgcagaa gaactccaga acagcatcca gacacgcttt
     4201 gaagtagaaa atagcacaga gagataacgc tcaggacagg ataccgaacg gcacaacaga
     4261 gcgtaaggag aaaatgtcac ataaggcgct cttccgcttc ctcgctcact gactcgctac
     4321 gctcggacgt tcgactgcgg cgagcggtgt cagctcactc aaaagcggta atacggttat
     4381 ccacagaatc aggggataaa gccggaaaga acatgtgagc aaaaagcaaa gcaccggaag
     4441 aagccagcga cgcaggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat
     4501 cgacgctcaa gccagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc
     4561 cctggaagct ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc
     4621 gcctttctcc cttcgggaag cgtggcgctt tctcatagct cacgctgttg gtatctcggc
     4681 tcggtgtagg tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac
     4741 cgctgcgcct tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttagcg
     4801 ccactggcag cagccgttgg taacttggtt agcagagcga tgatggcgca aatggtgcaa
     4861 cagagttctt gaagtagtgg cccgactacg gctacactgg aaggacagta tttggtatct
     4921 gcgctctgct gaagccagtt acctcggtta agcagttccc caactgactt aaccttcgat
     4981 caaaccgcct ccccaggcgg ttttttcgtt tacaggcagc agattacgcg cagaaaaaaa
     5041 ggatctcaag aagatccttt gatcttttct actgaacaga gatccccgtc aatttagaag
     5101 aagatgatgg agccacagtc cctccctgaa catcacgtat atagttagcc tga
//
