LOCUS       NZ_CP051722             5153 bp    DNA     linear   CON 13-JUN-2023
DEFINITION  Escherichia coli strain SCU-116 plasmid pSCU-116-3, complete
            sequence.
ACCESSION   NZ_CP051722
VERSION     NZ_CP051722.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14609778
            Assembly: GCF_012934555.1
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., 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  JOURNAL   Unpublished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 5153)
  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                   :: 21x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/13/2023 01:49:14
            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)                     :: 5,046
            CDSs (total)                      :: 4,924
            Genes (coding)                    :: 4,721
            CDSs (with protein)               :: 4,721
            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)              :: 203
            CDSs (without protein)            :: 203
            Pseudo Genes (ambiguous residues) :: 0 of 203
            Pseudo Genes (frameshifted)       :: 62 of 203
            Pseudo Genes (incomplete)         :: 141 of 203
            Pseudo Genes (internal stop)      :: 43 of 203
            Pseudo Genes (multiple problems)  :: 41 of 203
            Pseudo Genes (short protein)      :: 4 of 203
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP051722.1.
            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-116"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-116-3"
                     /geo_loc_name="USA: California"
                     /collection_date="2015"
     gene            complement(<1..95)
                     /locus_tag="HHJ31_RS24920"
                     /old_locus_tag="HHJ31_24935"
     CDS             complement(<1..95)
                     /locus_tag="HHJ31_RS24920"
                     /old_locus_tag="HHJ31_24935"
                     /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_077108132.1"
                     /translation="MRKRFFVGIFAINLLVGCQANYIRDVQGGTVA"
                     /name="colicin release lysis protein"
     gene            143..484
                     /locus_tag="HHJ31_RS24925"
                     /old_locus_tag="HHJ31_24940"
     CDS             143..484
                     /locus_tag="HHJ31_RS24925"
                     /old_locus_tag="HHJ31_24940"
                     /inference="COORDINATES: protein motif:HMM:NF015489.2"
                     /GO_function="GO:0015643 - toxic substance binding
                     [Evidence IEA]"
                     /GO_process="GO:0030153 - bacteriocin immunity [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin E1 family microcin immunity protein"
                     /protein_id="WP_000058755.1"
                     /translation="MSLRYYIKNILFGLYCALIYIYLITKNNEGYYFLASDKMLYAIVI
                     STILCPYSKYAIEHIFFKFIKKDFFRKRKNLNNAPVAKLNLFMLYNLLCLVLAIPFGLL
                     GLFISIKNN"
                     /name="colicin E1 family microcin immunity protein"
     gene            complement(481..2046)
                     /locus_tag="HHJ31_RS24930"
                     /old_locus_tag="HHJ31_24945"
     CDS             complement(481..2046)
                     /locus_tag="HHJ31_RS24930"
                     /old_locus_tag="HHJ31_24945"
                     /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_023150412.1"
                     /translation="METAVAYYKDGVPYDDKGQVIITLLNGNPDGSGSGGGGGTGGSKS
                     ESSAAIHATAKWSTAQLKKTQAEQAARAKAAAEAQAKAKANRDALTQHLKDIVNEALRH
                     NSTHPEVIDLAHANNAAMQAEAERLRLAKAEEKARKEAEAAEKSFQEAEQRRKEIEKEQ
                     AETERQLKLAEDEEKRLAALSEEARAVEVAQKNLAAAQSELAKVDEEINTLNTRLSSSI
                     HARDAETNTLSGKRNELDQASAKYKELDERVKLLSPRANDPLQSRPFFEATRLRARAGD
                     EMEEKQKQVTASETRLNQISSEINGIQEAISQANNKRSTAVSRIHDAEDNLKTAQTNLL
                     NSQIKDAVDATVSFYQTLSEKYGEKYSKMAQELADKSKGKKISNVNEALAAFEKYKDVL
                     NKKFSKADRDAIFNALEAVKYEDWAKHLDQFAKYLKITGHVSFGYDVVSDILKIKDTGD
                     WKPLFLTLEKKAVDAGVSYVVVLLFSVLAGTTLGIWGIAIVTGILCAFIDKNKLNTINE
                     VLGI"
                     /name="colicin-like pore-forming protein"
     gene            2306..2743
                     /locus_tag="HHJ31_RS24935"
                     /old_locus_tag="HHJ31_24950"
     CDS             2306..2743
                     /locus_tag="HHJ31_RS24935"
                     /old_locus_tag="HHJ31_24950"
                     /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            2824..3243
                     /locus_tag="HHJ31_RS24940"
                     /old_locus_tag="HHJ31_24955"
     CDS             2824..3243
                     /locus_tag="HHJ31_RS24940"
                     /old_locus_tag="HHJ31_24955"
                     /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(3468..3791)
                     /gene="mobA"
                     /locus_tag="HHJ31_RS24945"
                     /old_locus_tag="HHJ31_24960"
     CDS             complement(3468..3791)
                     /gene="mobA"
                     /locus_tag="HHJ31_RS24945"
                     /old_locus_tag="HHJ31_24960"
                     /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            4075..4269
                     /locus_tag="HHJ31_RS24950"
                     /old_locus_tag="HHJ31_24965"
     CDS             4075..4269
                     /locus_tag="HHJ31_RS24950"
                     /old_locus_tag="HHJ31_24965"
                     /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"
     Typing          complement(3801..4040)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="7.6e-123"
     Typing          4299..4828
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.59"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          complement(3472..3791)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="3.11e-62"
ORIGIN
        1 gccacagtcc ctccctgaac atcacgtata tagttagcct gacatccaac aaggaggttt
       61 atagcgaata ttcccacaaa aaatcttttc ctcataactc gatccttata aaatgaaaag
      121 aatatataac gaggtttaat ttatgagttt aagatactac ataaaaaata ttttgtttgg
      181 cctatactgc gcacttatat atatatacct tataacaaaa aacaacgaag ggtattattt
      241 cctagcgtca gataagatgc tatacgcaat agtgataagc actattctat gcccatattc
      301 aaaatatgct attgaacaca tattttttaa gttcataaag aaagattttt tcagaaaaag
      361 aaaaaaccta aataatgccc ccgtggcaaa attaaaccta tttatgctat acaatctact
      421 ttgtttggtc ctagcaatcc catttggatt gctaggactg tttatatcaa taaagaataa
      481 ttaaataccc aacacctcat ttatagtatt aagtttattc ttatcaataa aggcacatag
      541 aatgcctgta acaatagcaa tcccccagat acctaatgta gttccagcaa gcacactaaa
      601 aagtaaaaca acaacataac taactccagc atctacagct ttcttctcta atgtaagaaa
      661 tagcggcttc cagtcacctg tatccttaat ttttaggata tcagatacca catcatatcc
      721 aaaagaaaca tgtcccgtaa tcttcaagta cttggcaaac tgatctaaat gcttagccca
      781 gtcttcatac ttaaccgcct ccagtgcatt gaaaattgca tcacggtctg ctttgctgaa
      841 tttcttattt aatacatcct tgtatttctc aaaagcagct agagcttcat tcacattgct
      901 gattttctta cctttagatt tatcagcaag ttcctgtgcc atttttgaat atttttcacc
      961 atatttttca gatagcgttt gataaaagct aactgttgca tccacagcat ccttaatctg
     1021 cgagttcagg agattagtct gtgctgtttt caaattatct tcagcatcat gaatacgtga
     1081 aactgctgta cttcgcttat tattagcctg agaaatagcc tcttggattc catttatctc
     1141 agagctaatc tggttaagac gcgtttctga tgctgttacc tgcttttgtt tttcctccat
     1201 ctcatcacca gctctcgccc gtagtctggt ggcctcaaaa aaaggacgac tctgaagcgg
     1261 atcattcgcc ctaggagata aaagtttaac cctttcatcc agttctttat atttagcaga
     1321 tgcctgatcc aactcatttc gttttccgga cagcgtattc gtttctgcat cacgggcatg
     1381 aatactggag cttaaacggg tattgagcgt attaatctct tcatccactt tcgccagctc
     1441 agattgtgca gcagcaagat ttttttgtgc cacctccaca gcccgggcct cttcactcaa
     1501 tgctgccagg cgtttctctt catcctcagc cagtttcaat tggcgttctg tttcagcctg
     1561 ctccttctct atctctttac gtcgttgttc tgcttcctga aaagactttt ccgcagcttc
     1621 cgcttcttta cgggcttttt cttctgcttt tgcaaggcgc aaccgctctg cttctgcctg
     1681 catcgctgca ttattggcat gagccaggtc aataacctcc ggatgagtgg aattatggcg
     1741 aagcgcctca ttcacaatat ccttcagatg ttgagtcagc gcatcccggt ttgcttttgc
     1801 tttagcctgt gcttctgcgg cagcttttgc tcgggcagcc tgttctgcct gcgttttctt
     1861 caattgagca gtagaccatt tagctgtggc atgaatggct gcagaacttt cacttttgct
     1921 acctccagtt ccaccaccac cgccagagcc actcccgtct ggattaccat tcaaaagagt
     1981 aatgattacc tgccccttat catcataagg aacaccatct ttatagtacg ctacagctgt
     2041 ttccattata aaatcctctt tgacattaaa aacaaatagt taaaagcaat atactgtata
     2101 tataatcact ggttttatat acagtttaaa attacgccgc tgcattttcc ctgtcaaccc
     2161 tgtggatttt catttttgtg aaaacgatca aaaaaacagc cacccacacc acgtgctatt
     2221 tccacccgat gccacaaaaa ccagcacaaa cattaccgtt ctcagacctc attatgtttt
     2281 actgaaacca tgagatgaga cacctatggg acactgtaac tttatggcat ggcacacact
     2341 ccgggacgca ctgaaaatga ctggaagatc gcgttcacag ttttaccgtg atatgcgctc
     2401 aggtcttgtc agttaccgta ccagccagga cggacgacgg gagtttgaaa ccagtgaact
     2461 gatccgggca tacggcgaat taaagcggaa tgagacacca gaaaggcaca ctcaaggaca
     2521 ctcagaaaaa cctcatgatc agcagacaga acgcattctc cgggaactga atgagctgaa
     2581 acaatgcctg acgctgatgc ttgaggataa acaagcccag gatacggagc gccggcgcca
     2641 ggaagcagaa cggaaacagc tacagaatga gatagcccag ctcaggcagg ctctggagca
     2701 ggaaaagaaa cggggattct ggtccaggct gttcggtcac tgaacgcgct cagaaactga
     2761 tgataagata atcttcggat aataactcac cgagaataaa tactttaagg tagggagaca
     2821 ctcatgagac gtaccggaaa caaactttgt cttatcgcca tgataacagc aacagtagct
     2881 ctcacagcct gtaccccaaa gggcagcgtg gaacaacata cccggcatta cgtatatgct
     2941 tctgatgacg gttttgatcc caacttttcc acccaaaaag ccgacacaac acgaatgatg
     3001 gtgccttttt ttcggcagtt ctgggatatg ggagctaaag ataaagcgac aggaaaatca
     3061 cggagtgatg tgcaacaacg cattcaacag tttcacagcc aggaattttt aaactcactc
     3121 cggggcacaa ctcaatttgc gggtactgat taccgcagca aagaccttac cccgaaaaaa
     3181 tccaggctgc tggctgacac gatttctgcg gtttatctcg atggctacga gggcagacag
     3241 taagtggatt taccataatc ccttaattgt acgcaccgct gaaacgcgct gaacgcaatt
     3301 ctgacgcaaa taccgcaaaa agagaggttt agccccgaaa aaacaggaag gatgcgtcag
     3361 gatcgttttc agctcactgc atagctatgc atgaaagcga atggtgatca ctttgggagc
     3421 ttacggtgtt cataccgtct gttttcgaca gttttctctc cgggaagcta atctgccata
     3481 agcctggata acagggcacg gtgatactcc gtaatagcga tcagcacctc cgcatactcc
     3541 ctgtccccga cacgcttgcc gtcgataaag agttttttct gtaacgcccc cagtctcata
     3601 acttctttca gtacccgatc atcagtcagt gagttaactt tcttaccgag agctgccgcc
     3661 cgtaaaaaac cggaaacggt cttgccgcat tcagcagccc tttttctgat ttcctggtct
     3721 tcttctgccg tcagacgaac agggcgactg atagcccgcc tgcgcgtatt acttccactt
     3781 cgttttgtca taaaacatgg ctccgtatct gacatgggtg tcggggcaaa gccctgacca
     3841 gggtaattgt aatagcgtgc atgtatgcgc ggtataacaa ttacacatcc tgtcctgtca
     3901 gcaagttcga attaccgaca aaggcacggc agttttttgg cagtgacagt attgtcaggc
     3961 agaaataccc gtcaaagcgt cagacggcag aataccggcg gtaaaacagt cgaaaagtgg
     4021 tacgcgatat aatcacacaa cgcagatgac agacagaacg gagaaaacga aaagatgaac
     4081 aagcagcagc aagccgtact caacatggca ggattcataa aaagccaaag cctgacgctg
     4141 ctcgaaaagc tggacgcact cgatgctgac gaacaggcta ccatgtgtga gaagctgcac
     4201 gaactcgcag aagaactcca gaacagcatc cagacacgct ttgaagtaga aaatagcaca
     4261 gagagataac gctcaggaca ggatgccgaa cggcacaaca gagcgtaagg agaaaatgtc
     4321 acataaggcg ctcttccgct tcctcgctca ctgactcgct acgctcggac gttcgactgc
     4381 ggcgagcggt gtcagctcac tcaaaagcgg taatacggtt atccacagaa tcaggggata
     4441 aagccggaaa gaacatgtga gcaaaaagca aagcaccgga agaagccagc gccgcaggcg
     4501 tttttccata ggctccgccc ccctgacgag catcacaaaa atcgacgctc aagccagagg
     4561 tggcgaaacc cgacaggact ataaagatac caggcgtttc cccctggaag ctccctcgtg
     4621 cgctctcctg ttccgaccct gccgcttacc ggatacctgt ccgcctttct cccttcggga
     4681 agcgtggcgc tttctcatag ctcacgctgt tggtatctcg gctcggtgta ggtcgttcgc
     4741 tccaagctgg gctgtgtgca cgaacccccc gttcagcccg accgctgcgc cttatccggt
     4801 aactatcgtc ttgagtccaa cccggtaaga cacgacttag cgccactggc agcagccgtt
     4861 ggtaacttgg ttagcagagc gatgatggcg caaatggtgc aacagagttc ttgaagtagt
     4921 ggcccgacta cggctacact ggaaggacag tatttggtat ctgcgctctg ctgaagccag
     4981 ttacctcggt taagcagttc cccaactgac ttaaccttcg atcaaaccgc ctccccaggc
     5041 ggttttttcg tttacaggca gcagattacg cgcagaaaaa aaggatctca agaagatcct
     5101 ttgatctttt ctactgaaca gagatccccg tcaatttaga agaagatgat gga
//
