LOCUS       NZ_CP051704             5153 bp    DNA     linear   CON 13-JUN-2023
DEFINITION  Escherichia coli strain SCU-125 plasmid pSCU-125-4, complete
            sequence.
ACCESSION   NZ_CP051704
VERSION     NZ_CP051704.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14609785
            Assembly: GCF_012934655.2
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  JOURNAL   Unpublished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                   :: 14x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/13/2023 04:29:13
            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)                     :: 5,227
            CDSs (total)                      :: 5,100
            Genes (coding)                    :: 4,890
            CDSs (with protein)               :: 4,890
            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)              :: 210
            CDSs (without protein)            :: 210
            Pseudo Genes (ambiguous residues) :: 0 of 210
            Pseudo Genes (frameshifted)       :: 76 of 210
            Pseudo Genes (incomplete)         :: 138 of 210
            Pseudo Genes (internal stop)      :: 44 of 210
            Pseudo Genes (multiple problems)  :: 43 of 210
            Pseudo Genes (short protein)      :: 3 of 210
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP051704.1.
            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-125"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-125-4"
                     /geo_loc_name="USA: California"
                     /collection_date="2016"
     gene            30..371
                     /locus_tag="HHJ38_RS25930"
                     /old_locus_tag="HHJ38_25965"
     CDS             30..371
                     /locus_tag="HHJ38_RS25930"
                     /old_locus_tag="HHJ38_25965"
                     /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(368..1933)
                     /locus_tag="HHJ38_RS25935"
                     /old_locus_tag="HHJ38_25970"
     CDS             complement(368..1933)
                     /locus_tag="HHJ38_RS25935"
                     /old_locus_tag="HHJ38_25970"
                     /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            2193..2630
                     /locus_tag="HHJ38_RS25940"
                     /old_locus_tag="HHJ38_25975"
     CDS             2193..2630
                     /locus_tag="HHJ38_RS25940"
                     /old_locus_tag="HHJ38_25975"
                     /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            2711..3130
                     /locus_tag="HHJ38_RS25945"
                     /old_locus_tag="HHJ38_25980"
     CDS             2711..3130
                     /locus_tag="HHJ38_RS25945"
                     /old_locus_tag="HHJ38_25980"
                     /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(3355..3678)
                     /gene="mobA"
                     /locus_tag="HHJ38_RS25950"
                     /old_locus_tag="HHJ38_25985"
     CDS             complement(3355..3678)
                     /gene="mobA"
                     /locus_tag="HHJ38_RS25950"
                     /old_locus_tag="HHJ38_25985"
                     /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            3962..4156
                     /locus_tag="HHJ38_RS25955"
                     /old_locus_tag="HHJ38_25990"
     CDS             3962..4156
                     /locus_tag="HHJ38_RS25955"
                     /old_locus_tag="HHJ38_25990"
                     /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(4998..5135)
                     /locus_tag="HHJ38_RS25970"
                     /old_locus_tag="HHJ38_26005"
     CDS             complement(4998..5135)
                     /locus_tag="HHJ38_RS25970"
                     /old_locus_tag="HHJ38_26005"
                     /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"
     Typing          complement(3688..3927)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="7.6e-123"
     Typing          4186..4715
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.59"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          complement(3359..3678)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="3.11e-62"
ORIGIN
        1 tgaaaagaat atataacgag gtttaattta tgagtttaag atactacata aaaaatattt
       61 tgtttggcct atactgcgca cttatatata tataccttat aacaaaaaac aacgaagggt
      121 attatttcct agcgtcagat aagatgctat acgcaatagt gataagcact attctatgcc
      181 catattcaaa atatgctatt gaacacatat tttttaagtt cataaagaaa gattttttca
      241 gaaaaagaaa aaacctaaat aatgcccccg tggcaaaatt aaacctattt atgctataca
      301 atctactttg tttggtccta gcaatcccat ttggattgct aggactgttt atatcaataa
      361 agaataatta aatacccaac acctcattta tagtattaag tttattctta tcaataaagg
      421 cacatagaat gcctgtaaca atagcaatcc cccagatacc taatgtagtt ccagcaagca
      481 cactaaaaag taaaacaaca acataactaa ctccagcatc tacagctttc ttctctaatg
      541 taagaaatag cggcttccag tcacctgtat ccttaatttt taggatatca gataccacat
      601 catatccaaa agaaacatgt cccgtaatct tcaagtactt ggcaaactga tctaaatgct
      661 tagcccagtc ttcatactta accgcctcca gtgcattgaa aattgcatca cggtctgctt
      721 tgctgaattt cttatttaat acatccttgt atttctcaaa agcagctaga gcttcattca
      781 cattgctgat tttcttacct ttagatttat cagcaagttc ctgtgccatt tttgaatatt
      841 tttcaccata tttttcagat agcgtttgat aaaagctaac tgttgcatcc acagcatcct
      901 taatctgcga gttcaggaga ttagtctgtg ctgttttcaa attatcttca gcatcatgaa
      961 tacgtgaaac tgctgtactt cgcttattat tagcctgaga aatagcctct tggattccat
     1021 ttatctcaga gctaatctgg ttaagacgcg tttctgatgc tgttacctgc ttttgttttt
     1081 cctccatctc atcaccagct ctcgcccgta gtctggtggc ctcaaaaaaa ggacgactct
     1141 gaagcggatc attcgcccta ggagataaaa gtttaaccct ttcatccagt tctttatatt
     1201 tagcagatgc ctgatccaac tcatttcgtt ttccggacag cgtattcgtt tctgcatcac
     1261 gggcatgaat actggagctt aaacgggtat tgagcgtatt aatctcttca tccactttcg
     1321 ccagctcaga ttgtgcagca gcaagatttt tttgtgccac ctccacagcc cgggcctctt
     1381 cactcaatgc tgccaggcgt ttctcttcat cctcagccag tttcaattgg cgttctgttt
     1441 cagcctgctc cttctctatc tctttacgtc gttgttctgc ttcctgaaaa gccttttccg
     1501 cagcttccgc ttctttacgg gctttttctt ctgcttttgc aaggcgcaac cgctctgctt
     1561 ctgcctgcat cgctgcatta ttggcatgag ccaggtcaat aacctccgga tgagtggaat
     1621 tatggcgaag cgcctcattc acaatatcct tcagatgttg agtcagcgca tcccggtttg
     1681 cttttgcttt agcctgtgct tctgcggcag cttttgctcg ggcagcctgt tctgcctgcg
     1741 ttttcttcaa ttgagcagta gaccatttag ctgtggcatg aatggctgca gaactttcac
     1801 ttttgctacc tccagttcca ccaccaccgc cagagccact cccgtctgga ttaccattca
     1861 aaagagtaat gattacctgc cccttatcat cataaggaac accatcttta tagtacgcta
     1921 cagctgtttc cattataaaa tcctctttga cattaaaaac aaatagttaa aagcaatata
     1981 ctgtatatat aatcactggt tttatataca gtttaaaatt acgccgctgc attttccctg
     2041 tcaaccctgt ggattttcat ttttgtgaaa acgatcaaaa aaacagccac ccacaccacg
     2101 tgctatttcc acccgatgcc acaaaaacca gcacaaacat taccgttctc agacctcatt
     2161 atgttttact gaaaccatga gatgagacac ctatgggaca ctgtaacttt atggcatggc
     2221 acacactccg ggacgcactg aaaatgactg gaagatcgcg ttcacagttt taccgtgata
     2281 tgcgctcagg tcttgtcagt taccgtacca gccaggacgg acgacgggag tttgaaacca
     2341 gtgaactgat ccgggcatac ggcgaattaa agcggaatga gacaccagaa aggcacactc
     2401 aaggacactc agaaaaacct catgatcagc agacagaacg cattctccgg gaactgaatg
     2461 agctgaaaca atgcctgacg ctgatgcttg aggataaaca agcccaggat acggagcgcc
     2521 ggcgccagga agcagaacgg aaacagctac agaatgagat agcccagctc aggcaggctc
     2581 tggagcagga aaagaaacgg ggattctggt ccaggctgtt cggtcactga acgcgctcag
     2641 aaactgatga taagataatc ttcggataat aactcaccga gaataaatac tttaaggtag
     2701 ggagacactc atgagacgta ccggaaacaa actttgtctt atcgccatga taacagcaac
     2761 agtagctctc acagcctgta ccccaaaggg cagcgtggaa caacataccc ggcattacgt
     2821 atatgcttct gatgacggtt ttgatcccaa cttttccacc caaaaagccg acacaacacg
     2881 aatgatggtg cctttttttc ggcagttctg ggatatggga gctaaagata aagcgacagg
     2941 aaaatcacgg agtgatgtgc aacaacgcat tcaacagttt cacagccagg aatttttaaa
     3001 ctcactccgg ggcacaactc aatttgcggg tactgattac cgcagcaaag accttacccc
     3061 gaaaaaatcc aggctgctgg ctgacacgat ttctgcggtt tatctcgatg gctacgaggg
     3121 cagacagtaa gtggatttac cataatccct taattgtacg caccactgaa acgcgctgaa
     3181 cgcgattctg acgcagacac cgcaaaaaga gatgttttac cccggaaaaa caggaaggat
     3241 gcgtcaggat cgttttcagc tctctgcata gctatgcatg aaagcgaatg gtgatcactt
     3301 tgggagctta cggtgttcat accgtcagtt ttcgacagtt ttctctccgg gaagctaatc
     3361 tgccataagc ctggataaca gggcacggtg atactccgta atagcgatca gcacctccgc
     3421 atactccctg tccccgacac gcttgccgtc gataaagagt tttttctgta acgcccccag
     3481 tctcataact tctttcagta cccgatcatc agtcagtgag ttaactttct taccgagagc
     3541 tgccgcccgt aaaaaaccgg aaacggtctt gccgcattca gcagcccttt ttctgatttc
     3601 ctggtcttct tctgccgtca gacgaacagg gcgactgata gcccgcctgc gcgtattact
     3661 tccacttcgt tttgtcataa aacatggctc cgtatctgac atgggtgtcg gggcaaagcc
     3721 ctgaccaggg taattgtaat agcgtgcatg tatgcgcggt ataacaatta cacatcctgt
     3781 cctgtcagca agttcgaatt accgacaaag gcacggcagt tttttggcag tgacagtatt
     3841 gtcaggcaga aatacccgtc aaagcgtcag acggcagaat accggcggta aaacagtcga
     3901 aaagtggtac gcgatataat cacacaacgc agatgacaga cagaacggag aaaacgaaaa
     3961 gatgaacaag cagcagcaag ccgtactcaa catggcagga ttcataaaaa gccaaagcct
     4021 gacgctgctc gaaaagctgg acgcactcga tgctgacgaa caggctacca tgtgtgagaa
     4081 gctgcacgaa ctcgcagaag aactccagaa cagcatccag acacgctttg aagtagaaaa
     4141 tagcacagag agataacgct caggacagga tgccgaacgg cacaacagag cgtaaggaga
     4201 aaatgtcaca taaggcgctc ttccgcttcc tcgctcactg actcgctacg ctcggacgtt
     4261 cgactgcggc gagcggtgtc agctcactca aaagcggtaa tacggttatc cacagaatca
     4321 ggggataaag ccggaaagaa catgtgagca aaaagcaaag caccggaaga agccagcgcc
     4381 gcaggcgttt ttccataggc tccgcccccc tgacgagcat cacaaaaatc gacgctcaag
     4441 ccagaggtgg cgaaacccga caggactata aagataccag gcgtttcccc ctggaagctc
     4501 cctcgtgcgc tctcctgttc cgaccctgcc gcttaccgga tacctgtccg cctttctccc
     4561 ttcgggaagc gtggcgcttt ctcatagctc acgctgttgg tatctcggct cggtgtaggt
     4621 cgttcgctcc aagctgggct gtgtgcacga accccccgtt cagcccgacc gctgcgcctt
     4681 atccggtaac tatcgtcttg agtccaaccc ggtaagacac gacttagcgc cactggcagc
     4741 agccgttggt aacttggtta gcagagcgat gatggcgcaa atggtgcaac agagttcttg
     4801 aagtagtggc ccgactacgg ctacactgga aggacagtat ttggtatctg cgctctgctg
     4861 aagccagtta cctcggttaa gcagttcccc aactgactta accttcgatc aaaccgcctc
     4921 cccaggcggt tttttcgttt acaggcagca gattacgcgc agaaaaaaag gatctcaaga
     4981 agatcctttg atcttttcta ctgaacagag atccccgtca atttagaaga agatgatgga
     5041 gccacagtcc ctccctgaac atcacgtata tagttagcct gacatccaac aaggaggttt
     5101 atagcgaata ttcccacaaa aaatcttttc ctcataactc gatccttata aaa
//
