LOCUS       NZ_CP053244             3131 bp    DNA     linear   CON 13-JUN-2023
DEFINITION  Escherichia coli strain SCU-106 plasmid pSCU-106-10, complete
            sequence.
ACCESSION   NZ_CP053244
VERSION     NZ_CP053244.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14609771
            Assembly: GCF_013085185.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3131)
  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  JOURNAL   Unpublished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 3131)
  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 03:10:47
            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)                     :: 5,452
            CDSs (total)                      :: 5,328
            Genes (coding)                    :: 5,059
            CDSs (with protein)               :: 5,059
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 269
            CDSs (without protein)            :: 269
            Pseudo Genes (ambiguous residues) :: 0 of 269
            Pseudo Genes (frameshifted)       :: 108 of 269
            Pseudo Genes (incomplete)         :: 154 of 269
            Pseudo Genes (internal stop)      :: 52 of 269
            Pseudo Genes (multiple problems)  :: 47 of 269
            Pseudo Genes (short protein)      :: 3 of 269
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP053244.1.
            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..3131
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-106"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-106-10"
                     /geo_loc_name="USA: California"
                     /collection_date="2015"
     gene            complement(104..532)
                     /gene="mobA"
                     /locus_tag="HHJ24_RS26955"
                     /old_locus_tag="HHJ24_26950"
     CDS             complement(104..532)
                     /gene="mobA"
                     /locus_tag="HHJ24_RS26955"
                     /old_locus_tag="HHJ24_26950"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001107325.1"
                     /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_032311188.1"
                     /translation="MTKNKRSGSEVRQRTKVITLRVNNRIANEIRRRAKLEGLTISEYI
                     RTASLNNEIKQRVPSRYLDELIKLGRMQKNLFDKGKRPKDKEYLDVMHKIISLCGEMKT
                     VTQRISDIYNEMDLIKQEIKIIKRDHKNKYPGSNLFNR"
                     /name="mobA"
     gene            complement(1265..1444)
                     /locus_tag="HHJ24_RS26960"
                     /old_locus_tag="HHJ24_26955"
     CDS             complement(1265..1444)
                     /locus_tag="HHJ24_RS26960"
                     /old_locus_tag="HHJ24_26955"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_225391470.1"
                     /translation="MPTDARQGMEGAKNAYSGSQEVRRADTPNQGLSGRQEPRQPPCKA
                     HLHGTDSHSVGRWS"
                     /name="hypothetical protein"
     gene            1857..2387
                     /locus_tag="HHJ24_RS26965"
                     /old_locus_tag="HHJ24_26960"
     CDS             1857..2387
                     /locus_tag="HHJ24_RS26965"
                     /old_locus_tag="HHJ24_26960"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000007848.1"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA];
                     GO:0006276 - plasmid maintenance [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="WP_032311190.1"
                     /translation="MINSRYKTNPFLEGMIVPVKGKQVRLSRLGRDENILVNQNTGEVQ
                     GTHVTTYKRVDGEQFVKLFTANIALTFDLSAQGIKAFNVLMWAMQKQSVSKDEVFLDTH
                     IREEFLAVYNDKDKPIKLSQPTFARGLAELTKAQIIAKTIRQGVYWINPNFAFNGDRIA
                     FTTLIERQSNNEK"
                     /name="replication/maintenance protein RepL"
     gene            2401..>3131
                     /locus_tag="HHJ24_RS26970"
                     /old_locus_tag="HHJ24_26965"
     CDS             2401..>3131
                     /locus_tag="HHJ24_RS26970"
                     /old_locus_tag="HHJ24_26965"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_170969623.1"
                     /translation="MRKKNMFPPGSLSIKLNNPLTKYEIIEILSEYLSMLEITFGIKEF
                     RLFSYLECVLNGEKQAIYHKGNNAIVSGFSLDSMEDINNRKINKIMLGCDDFDAMQKID
                     NMLNMKAEPNPYEHFKSFLSLVPANLAYDLIRKTDELVELERMEKIKEKNELREKKREK
                     DKNILKIIYNNKIAEYSCTFDYFRSVYLSSSGFLSLEKQKAKYFLAEGLDSLLNDYVGK
                     RLVRLSIKGDDGKVSIVEIYD"
                     /name="hypothetical protein"
ORIGIN
        1 aaatggtaaa tttttattta agacaaaacc tctaaataaa acatagagta atctttaata
       61 tgtttagccg atatatcaaa taagatgata tatcggctaa tatttatcta ttaaataaat
      121 tagagcctgg gtatttattt ttgtgatctc tttttattat ttttatttcc tgttttatta
      181 aatccatttc attatatata tcagaaattc gctgcgttac tgttttcatc tcaccgcaaa
      241 gtgaaattat tttatgcatc acatcaagat actctttgtc cttcggcctc ttccctttat
      301 caaataaatt cttctgcatc cgaccaagtt taattaattc atccagatat ctggaaggca
      361 cgcgctgttt tatttcatta tttaaacttg ccgtccttat atattctgaa atagtcagcc
      421 cttcgagctt cgctcgccgc ctgatttcgt ttgcgattct gttatttact ctaagggtga
      481 taaccttagt cctctgccgt acttctgaac cactacgctt atttttagtc atcgtaatga
      541 ctctccattt tgcacgtttg gggtgtcggg gcttgccctg acaggaggta ttctcatgca
      601 agcgaatgta ttcgcggtat gacgaataca catcctgtcc cgttttccgc tacaactttt
      661 cgacgaaaat aaaataccgc gtcgtaacct ggtatttctg atacaaaaaa atgatgcttc
      721 attcaatatt atttacacag attttaaaag ttatcatttg ttatttgata aataacgcct
      781 tattaattga ttcctttgtc cattttcgtt tgtgtcttat ttatgaaata aagattatga
      841 cttcctaaat atatgattac ttgcctgtta gtgatgcggt aggtatccag agaacaggaa
      901 gcagaagaac aagataattg catatgtata aaatataaca ctgtgagtta ttgatatggc
      961 gtttatatat taaaaatata acttaacatc ccgcttaata tttattttct cctagcaatg
     1021 ggagcattaa tccccgtgta gtgctctgcc agctgctgac aacctcgaca tacaaccatc
     1081 gatgcgatag aacatcaggg cgcgtttccg gcaaaaacta accatgggga tggtttgcgt
     1141 gccaacgaac gccggaaacg cgcctcaaac ccaccgagcc gccacggttc cggcagcgcc
     1201 ttgagcgcaa ccggaaaccg tctggggaga cccccagccc ccccctcgct gtaacaccga
     1261 cggtctacga ccacctacca accgagtggc tgtctgttcc gtgcaaatgg gctttgcagg
     1321 ggggctggcg cggttcctgg cgacctgaaa gcccctggtt aggggtatcg gcgcgcctga
     1381 cctcctgaga gccactgtaa gcgtttttcg cgccttccat gccctgacgg gcatctgttg
     1441 gcatttgatc gcgtctggga gcttctgagc gcgtttaagg gccaaagacg accaaaccct
     1501 caaaaacgcg ttttggaatg tctgagagct tgcaaacggc gcgatcgtca cggatcaaaa
     1561 acgggatcga cggcaatgcg cgagtgttgg taccgctcgc cgcaagtcga tgaccgaacg
     1621 tagtgagcga atcgacgagg aagcggaaga gaaccgacag ctaaattgag cacttacgca
     1681 ctgccgttaa gaactaagaa gggagtattg cggaagccgc gaaaaatggg gatcgaattt
     1741 tcagatcatg tgagacggtc tatcagacgt cctcagacgg tctatcaaaa atatcgttga
     1801 ttttgataga ccgggattct aagattgaat cccgtctatc aaaaaaagga ttaattgtga
     1861 taaacagtcg atacaaaact aacccttttt tagagggtat gatagtgccc gtcaagggta
     1921 aacaagtcag actttcccgt ctaggtcgag atgaaaacat actggttaat cagaacacgg
     1981 gagaggttca aggtacccat gtaacaacat ataaacgggt tgatggtgag cagtttgtaa
     2041 aactattcac tgcaaatatc gcgttaacct ttgatttgtc agctcaagga ataaaagcat
     2101 ttaacgtttt gatgtgggca atgcaaaagc agtcagtatc aaaagacgaa gtttttttag
     2161 atactcacat aagagaggag tttcttgctg tttataatga taaagataaa ccaattaaat
     2221 taagtcagcc aacatttgct agaggattag ctgaacttac caaagctcaa attatagcga
     2281 aaaccatacg tcaaggagtg tattggataa atccaaattt tgcattcaac ggtgatagaa
     2341 tagcgtttac aactcttatt gaaaggcaaa gcaataatga aaaataacag ggtaaaaata
     2401 atgagaaaga aaaatatgtt cccgccaggt tctttgagta taaaattaaa caatccttta
     2461 actaaatatg aaataattga gatattatca gaatatctat ctatgttaga aataactttt
     2521 gggataaagg aatttaggct tttttcttat ttggaatgcg tgctcaatgg agaaaaacag
     2581 gctatatacc ataaaggtaa taacgcaatc gtgtctggat tttcacttga ttcaatggag
     2641 gatataaaca ataggaaaat caataagata atgcttggtt gcgatgattt tgatgccatg
     2701 caaaaaatcg ataatatgtt aaatatgaaa gctgaaccaa atccgtatga acattttaag
     2761 agttttttat cactagttcc tgctaatctt gcatatgatc tcatcaggaa aaccgacgag
     2821 ttagtcgaac ttgagagaat ggaaaaaata aaagaaaaaa acgaattacg tgaaaagaaa
     2881 cgagaaaaag ataaaaacat attaaagatt atttataaca ataagatagc tgagtattca
     2941 tgtacttttg attattttag atctgtatat ttatctagct ctggtttttt atctttagaa
     3001 aaacaaaagg ctaaatattt tcttgcggaa gggttagatt cactcctaaa tgattatgtt
     3061 ggtaaaaggt tggtaagatt atcaattaaa ggcgatgatg gtaaagtttc catagtcgaa
     3121 atatatgatg a
//
