LOCUS       NZ_CP051851             4980 bp    DNA     linear   CON 10-JAN-2024
DEFINITION  Escherichia coli strain SCU-101 plasmid pSCU-101-2, complete
            sequence.
ACCESSION   NZ_CP051851
VERSION     NZ_CP051851.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14609767
            Assembly: GCF_017815815.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4980)
  AUTHORS   Stephens,C., Arismendi,T., Wright,M., Hartman,A., Gonzalez,A.,
            Gill,M., Pandori,M. and Hess,D.
  TITLE     F Plasmids Are the Major Carriers of Antibiotic Resistance Genes in
            Human-Associated Commensal Escherichia coli
  JOURNAL   mSphere 5 (4), e00709-20 (2020)
   PUBMED   32759337
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 4980)
  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                   :: 91x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/10/2024 02:10:20
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,245
            CDSs (total)                      :: 5,129
            Genes (coding)                    :: 4,868
            CDSs (with protein)               :: 4,868
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 261
            CDSs (without protein)            :: 261
            Pseudo Genes (ambiguous residues) :: 0 of 261
            Pseudo Genes (frameshifted)       :: 122 of 261
            Pseudo Genes (incomplete)         :: 165 of 261
            Pseudo Genes (internal stop)      :: 60 of 261
            Pseudo Genes (multiple problems)  :: 74 of 261
            Pseudo Genes (short protein)      :: 5 of 261
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP051851.1.
            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..4980
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-101"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-101-2"
                     /geo_loc_name="USA: California"
                     /collection_date="2015"
     gene            complement(834..1025)
                     /locus_tag="HHJ20_RS25910"
                     /old_locus_tag="HHJ20_25905"
     CDS             complement(834..1025)
                     /locus_tag="HHJ20_RS25910"
                     /old_locus_tag="HHJ20_25905"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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_001401730.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGEAL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(1860..2288)
                     /locus_tag="HHJ20_RS25915"
                     /old_locus_tag="HHJ20_25910"
     CDS             complement(1860..2288)
                     /locus_tag="HHJ20_RS25915"
                     /old_locus_tag="HHJ20_25910"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000830439.1"
                     /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_042089515.1"
                     /translation="MKRSGGTRYMYLSALITVAAALTACTPKTSLEQHTRHYVYASDDG
                     FDPNFYTKKADTTRMMIPFFQQFREMGVKDKAAGVSAETAQQRIKEFHSEEFLQSLRTT
                     TTFAGRKYTNGDMPSPEKMKLLADTISAVYLDGYEGRQ"
                     /name="Exc2 family lipoprotein"
     gene            complement(2369..2806)
                     /locus_tag="HHJ20_RS25920"
                     /old_locus_tag="HHJ20_25915"
     CDS             complement(2369..2806)
                     /locus_tag="HHJ20_RS25920"
                     /old_locus_tag="HHJ20_25915"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001405929.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="entry exclusion protein 1"
                     /protein_id="WP_170981958.1"
                     /translation="MGHCHFMAWHTLQDALKMTGRSRSQFYRDMRAGLVSYRTSQDGRR
                     EFETSELIRAYGELKRNETPERHTAGQAEKPHDQQTERILRELNELKQCLTLMLEDKQA
                     QDTERQRQEAEREQLQNEIAQLRQALEQEKKRGVWSRLFGR"
                     /name="entry exclusion protein 1"
     gene            3066..4292
                     /locus_tag="HHJ20_RS25925"
                     /old_locus_tag="HHJ20_25920"
     CDS             3066..4292
                     /locus_tag="HHJ20_RS25925"
                     /old_locus_tag="HHJ20_25920"
                     /inference="COORDINATES: protein motif:HMM:NF013211.4"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_function="GO:0140911 - pore-forming activity [Evidence
                     IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA];
                     GO:0050829 - defense response to Gram-negative bacterium
                     [Evidence IEA]; GO:0031640 - killing of cells of another
                     organism [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_052232694.1"
                     /translation="MAKELGGYGPTAGESMGGTGANLNQQGGHNNSGVHWGGGSGHGNN
                     GGQGNTSSSNSTSTVMKPGESYLTPWGDVVINKDGLPVMNGVVMTEDNSSLVDNPLGGV
                     SRVLNSLISDMPSLFTKATGNNHDNNITAVNAVSPETRASDMEKSSKMVSALIDEKQNQ
                     KNQIAAQISEKNKKIEEMKKIFKHHSYHGITDLERDVDELQRKSNQLDADISKLYDYKN
                     TLKSDVDKIKDAVAYTATFYEKVTEKYGEKAELLAKSLADKANGKTIRGVDDALAAFDR
                     YRSSLGDKFNSADRAAIVAGIQALDATNTANSLAKYSKAFGYLGNAIDLADILVELKNA
                     LTTDNWRPVFVKLEIITANRAAVAISAIVFSIITGVPMGIVGFGVLVALAGSFFDEQLV
                     NEINSQLGI"
                     /name="colicin-like pore-forming protein"
     gene            4686..4826
                     /locus_tag="HHJ20_RS25930"
                     /old_locus_tag="HHJ20_25925"
     CDS             4686..4826
                     /locus_tag="HHJ20_RS25930"
                     /old_locus_tag="HHJ20_25925"
                     /inference="COORDINATES: protein motif:HMM:NF014457.4"
                     /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_153276082.1"
                     /translation="MKKMFFVGVVIISFCLVACQMNNIKGNSGGSFSSSNSGVGIQVKK
                     S"
                     /name="colicin release lysis protein"
     Typing          complement(132..676)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.698"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 accaaatact gtccttccag tgtagccgca gtcgggccac aacttcaaga actctgtagc
       61 accatttgtg ccatcatcgc tctgctaatc cggttaccag tggctgctgc cagtggcgtt
      121 aagtcgtgtc ttaccgggtt ggactcaaga cgatagttac cggataaggc gcagcggtcg
      181 ggctgaacgg ggggttcgtg cacacagccc agcttggagc gaacgaccta caccgagccg
      241 agataccaac agcgtgagct atgagaaagc gccacgcttc ccgaagggag aaaggcggac
      301 aggtatccgg taagcggcag ggtcggaaca ggagagcgca cgagggagct tccaggggga
      361 aacgcctggt atctttatag tcctgtcggg gttcgccacc tctgacttga gcgtcaattt
      421 ttgtgatgct cgtcaggggg gcggagccta tggaaaaacg ccagtggtgc ggctttcttc
      481 cggttcttgg tcttttgctc acatgttctt tccggcgtta tcccctgatt ctgtggataa
      541 ttgtattaca gcttttgagt gagtggactc cgctcgccgc agccgaacga ccgagcgcag
      601 cgagtcagtg agcgaggaag cggaagagcg cctgaactgg cattttctcc ttacgcatct
      661 gtgcggcatt tcacactgga catgccgcat ggttaagccc gtatacactc cgctatcgct
      721 acgtgactgg gtcatggctg cgccccgaca cccgctaaaa cccgttgacg ggcttgtctg
      781 ctcccggtat ccgctcacag gcaagctgta accgtctccg ggagctgcat gtgtcagagg
      841 gcttcaccgt catccccgaa acgtgcgagg caactgcggt aaagctcatc ggcgtggtcg
      901 tgaagcgatt cacagatatc tgcttgttca tctgcgtcca gttcgttgag cttctccagc
      961 agcgttaatg tctggcttct gatgaagcgc gccatgttca gagcggtttt ttcctgtttg
     1021 gtcactggtc tgatgtctcc gtgtaaggga atttctgttc atgggagcat gataactgtg
     1081 acgcaggcga gagtgataaa gctgagtgag cggttagtca ggggcgcaaa cattcgaacg
     1141 cggccagtgc gatgcaggat agggaaaacg ccgtaaaacg acgtcccttt cggcaatagc
     1201 aatatcatgg cacggcatat caactgataa ataattcctg tgcagtacag ccgctgttgc
     1261 ataaaatctc gctctgcggt gagtattgtt taatcaaaaa tccccgcagt tcttccagaa
     1321 aaacgcgagt ctgttctcat gcctgaaatg cccacacccc acgcaaaacc aactttttgc
     1381 tgatttgctt tttaaatcat gttgttatgg ttttaaaaat gtattttctt attcagattt
     1441 atacaaaagc acatcgtcga cgaccctatg gcgacgctat gacgacccta cttagggtca
     1501 gtactgacta tctgtagaaa aaacagttaa ttaatgtagg ggcgccccta ggggcgcgtc
     1561 gcctttttta catcacaccc ctgggggcgc tgccaggggt gtctgcccgg atatgtagca
     1621 atgagccagg gattcacgaa ctgaaaatgt ccgaaaatgt gcctcatggg caccgtatgc
     1681 gcccaaacag atcgctattc agtttcgtgc atagtcatgc aacgccctga aaacgatcct
     1741 gacgcatttt tccggttttc ctgggggtaa gcatttcttt ttgcggtgcc tgcgtcagaa
     1801 tcgcgctcaa cgcgttttaa tggtgcgtac aattaaggga ttatggtaaa tgtctccctt
     1861 tactgcctgc cctcgtagcc atcaagataa accgcagaaa tcgtgtcagc cagcagcttc
     1921 attttttccg gtgatggcat atcaccgttc gtgtattttc tgcccgcaaa ggtggttgtg
     1981 gttctcagtg actgaaggaa ttcttcagag tggaattctt ttatgcgttg ctgtgccgtt
     2041 tctgctgata ctccagctgc tttgtctttc acccccatct cccggaactg ctgaaagaac
     2101 ggaatcatca tccgtgtggt gtcagctttc ttggtgtaga agttaggatc aaacccatca
     2161 tctgaagcat aaacataatg ccgggtatgt tgttccaggc tggtttttgg ggtacaggcc
     2221 gtgagggctg ctgccacagt tatcagggcg ctaagataca tatagcgtgt gccgccagaa
     2281 cgtttcatgc gagtctcctt accttaaagt atttattttc ggtgagttat tatctgatgg
     2341 ctatcttatc atcagtctct gagtgcgttc agcgaccgaa caacctggac cagactcccc
     2401 gtttcttttc ctgctccagc gcctgcctga gctgggctat ctcattctgt agctgttccc
     2461 gttctgcttc ctggcgctgg cgctccgtat cctgagcttg tttatcctca agcatcagcg
     2521 tcaggcattg tttcagctcg ttcagctccc ggagaatgcg ttctgtctgc tgatcatgag
     2581 gtttttctgc ctgtcccgca gtgtgccttt ctggtgtctc attccgcttt aattcgccgt
     2641 atgcccggat cagttcactg gtttcaaact cccgtcgtcc gtcctggctt gtacggtaac
     2701 tgacaaggcc tgcgcgcata tcacggtaaa actgtgaacg cgatctgccc gtcattttca
     2761 gtgcgtcctg gagtgtgtgc catgccataa agtgacagtg tcccataggt gtctcatatc
     2821 atggtttcag taaaacatac tgaggccgga gaacggtaat gtttgtgctg gtttttgtgg
     2881 catcgggcgg gaatagctcg tggtgtgggg ggcttttttt ttgaacgttt tcacaaaaat
     2941 gaaaatccac agggttgaca gggaaaacgc agcggcgtaa ttttaagctg tatataaaac
     3001 cagtggttat atatacagta ttatggtttt aactatttat ttttaatgtc aaagaggtat
     3061 tttttatggc gaaagaactt ggtggatatg gcccaactgc cggtgaatct atggggggaa
     3121 caggggcgaa tttgaatcag caaggtggac ataataatag tggtgttcac tgggggggag
     3181 gctccggaca cggtaataat ggtggtcagg gtaatacaag ctcatcgaat tcaacatcga
     3241 cagtgatgaa gccaggtgag tcatatctaa ccccgtgggg agatgttgtt attaataaag
     3301 atggtctccc ggtgatgaat ggtgttgtta tgacagaaga taattcttct ttggttgata
     3361 atccattagg gggggtctcc agagttctta actctttaat tagtgatatg ccatcacttt
     3421 ttaccaaggc gacaggaaat aatcacgata ataacatcac tgctgttaat gcagtatctc
     3481 cagaaactcg agccagtgat atggagaaaa gttctaagat ggtgagtgct ctgattgatg
     3541 aaaagcagaa ccagaaaaat cagattgctg cgcagattag tgaaaaaaat aaaaaaatag
     3601 aggagatgaa aaaaatattc aagcatcact cctatcatgg aattactgat cttgaaaggg
     3661 atgttgatga gttacaaaga aaatctaatc agttggatgc tgatattagc aagttatatg
     3721 attacaaaaa cacattgaaa agcgatgtgg ataaaataaa ggatgctgtt gcctatacag
     3781 ctactttcta tgaaaaagta acagaaaagt atggtgagaa agctgaatta ttagcgaaaa
     3841 gtttggctga taaagctaat ggaaaaacta ttcgtggtgt tgatgatgct ttggctgcat
     3901 ttgatcggta tagaagttct ttgggtgata agtttaattc tgctgatcgt gccgctattg
     3961 tcgcaggaat tcaggcatta gatgctacga atacagcaaa cagtttagct aaatatagta
     4021 aagcatttgg ttatttagga aatgctattg atctggctga tattcttgtt gaacttaaaa
     4081 atgcattgac aacagataat tggcgacctg tttttgttaa actagaaatt attaccgcaa
     4141 atcgtgcagc cgtggctatt tctgcaattg ttttttctat tattacagga gttcctatgg
     4201 ggattgttgg ttttggtgtc cttgtggctt tagcaggctc tttttttgat gagcagttag
     4261 ttaatgaaat taactcgcaa ctaggtattt aatggttgtt aagctggtca ttttttttga
     4321 ccagcttgtc cttatctata aaaagataaa taatgctgaa tgggattgcg aaaataacac
     4381 aaaaaaacac atatataacg taaaatcgat taaccccatt ggagtttaac caagtggggt
     4441 tccaaaactg tattgatgta tatcttaatg ctactgtttt tacagtgtac atagatacag
     4501 gaagaagtat tccgctgagt atatatatga ttgatatttg tattgttttt gatgtcaatg
     4561 gttcgtggaa taagttatat attgcgataa gtataggaaa tagaccccat aataaacgag
     4621 agaaatagaa tttcttgttc atatgttaat gtctcactat cttgttttta tataaaggag
     4681 tatacatgaa gaaaatgttt tttgtaggtg ttgtaatcat atcattttgt ttggttgcat
     4741 gtcagatgaa taatattaaa ggtaattcag gtggttcatt ttcgtcatct aactcaggtg
     4801 tcggtatcca agtgaagaaa tcgtgagttt gcatcactga tcctcttgtg atccttttct
     4861 tctgcgcgta atctgctgct tgcaaacaaa aaaaccaccg ctaccaacgg tggtttgttt
     4921 gccggatcaa gagctaccaa ctctttttcc gaaggtaact ggcttcagca gagcgcagat
//
