LOCUS       NZ_CP051743             4802 bp    DNA     linear   CON 13-JUN-2023
DEFINITION  Escherichia coli strain SCU-105 plasmid pSCU-105-5, complete
            sequence.
ACCESSION   NZ_CP051743
VERSION     NZ_CP051743.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14609770
            Assembly: GCF_012934455.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4802)
  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  JOURNAL   Unpublished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 4802)
  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                   :: 57x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/13/2023 02:54:23
            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)                     :: 5,221
            CDSs (total)                      :: 5,101
            Genes (coding)                    :: 4,906
            CDSs (with protein)               :: 4,906
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 195
            CDSs (without protein)            :: 195
            Pseudo Genes (ambiguous residues) :: 0 of 195
            Pseudo Genes (frameshifted)       :: 64 of 195
            Pseudo Genes (incomplete)         :: 142 of 195
            Pseudo Genes (internal stop)      :: 39 of 195
            Pseudo Genes (multiple problems)  :: 44 of 195
            Pseudo Genes (short protein)      :: 4 of 195
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP051743.1.
            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..4802
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-105"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-105-5"
                     /geo_loc_name="USA: California"
                     /collection_date="2015"
     gene            complement(<1..391)
                     /locus_tag="HHJ23_RS25845"
                     /old_locus_tag="HHJ23_25860"
     CDS             complement(<1..391)
                     /locus_tag="HHJ23_RS25845"
                     /old_locus_tag="HHJ23_25860"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000135004.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_169063315.1"
                     /translation="MARVSISEAARLACVSRPTIYKLIKSGELSYTSVVKHGKAVKVID
                     TTELIRVFGSLSFDNERDHAVVKFDDRSTGVNSDFLQNLQHQVALLQAENAGLKDAVNA
                     RDEHINSLRQAMQLLEHKQGTADPQH"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(391..582)
                     /locus_tag="HHJ23_RS25850"
                     /old_locus_tag="HHJ23_25865"
     CDS             complement(391..582)
                     /locus_tag="HHJ23_RS25850"
                     /old_locus_tag="HHJ23_25865"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166327.1"
                     /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_024249396.1"
                     /translation="MTKPQKTALNMAKFIKGQTLLLLEKFNELELDAEADLCEKLHEDA
                     ELLCRTLTIRLDGHQGDL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1352..2740
                     /locus_tag="HHJ23_RS25855"
                     /old_locus_tag="HHJ23_25870"
     CDS             1352..2740
                     /locus_tag="HHJ23_RS25855"
                     /old_locus_tag="HHJ23_25870"
                     /inference="COORDINATES: protein motif:HMM:NF024573.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="AAA family ATPase"
                     /protein_id="WP_024475243.1"
                     /translation="MKIKVENLGFISSGEIDIKDLTIIFGKNNVGKTYLSYATYGILSR
                     LSSLSEGSTIVSKSDFNKLKADGSISIDTSKVASKEIIQKVNKDFTKSLSSFFNAKEDS
                     FKDANIEIEPNFTDSDLLKLSFSSNLNLDGTGVYSFNKSKNSSEIVISFVKLPEEATNK
                     SVGFAFGEDTIASILSSITSNLILKNIFKGLSRPFVITSERTGISLFYKEMDSHRSSLL
                     NHWITSKSSMSTPINKKLSAYSTPISDNINIIRQYESLTKRKSFLYSKRSKRSNRLMTE
                     TLESMLSGSFKHANGETIFTKKEDDKDVSIPMSISSSSVKSLFLLDLYIKHVAQYGDFL
                     VIDEPELNLHPENQVRMAELIVRLINLGIKIIMTTHSDYIIKEINNRIMLSNISKKENL
                     YDLSFRDEDVLRQDRVSAFTICDDRKIKEIQVDKYGINQEIFDDVISSLNERSDLIYDA
                     LCQE"
                     /name="AAA family ATPase"
     gene            2754..3350
                     /locus_tag="HHJ23_RS25860"
                     /old_locus_tag="HHJ23_25875"
     CDS             2754..3350
                     /locus_tag="HHJ23_RS25860"
                     /old_locus_tag="HHJ23_25875"
                     /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_024249394.1"
                     /translation="MISAIKKVIDDRVKIEIIKTANDHELVLKEESDGSDIEELRIINV
                     PEESFAFTLDYTSTSGSLKNIRLFKKLSCYVSSKNEDGINKSCDLVIVTKRDDGVKVVV
                     LDLKSKRTSGKRPTIQIENSILFLNYIFSLIDFYYKEEIGIAIDDIKYIKALVTTGPTQ
                     KTTVSKRPSKSSDVKKIPVKAMHKKATIRYSSIAA"
                     /name="hypothetical protein"
     gene            complement(3394..3585)
                     /locus_tag="HHJ23_RS26340"
     CDS             complement(3394..3585)
                     /locus_tag="HHJ23_RS26340"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001331458.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_224727947.1"
                     /translation="MCLMGTVCTQTVRHSLSCIAMQRAENDPDAFFWFSLDKASLFAVF
                     AAESRSARFSGTRNETLW"
                     /name="hypothetical protein"
     gene            4534..>4802
                     /locus_tag="HHJ23_RS25935"
     CDS             4534..>4802
                     /locus_tag="HHJ23_RS25935"
                     /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_211196912.1"
                     /translation="MKITTYLLRLSFELRLNMHLIVLNLQESAAILRSTKEQCRNIDSN
                     SMLLMWENFRFPNYPKLSGRPNAMAGMRGNGSTEFPKLPPGLCS"
                     /name="hypothetical protein"
     Typing          765..1120
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.118"
                     /coverage="82.0"
                     /evalue="1.79e-151"
     Typing          4148..4403
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.538"
                     /coverage="99.0"
                     /evalue="6.900000000000001e-74"
ORIGIN
        1 catgctgcgg atcagcagtg ccctgcttat gctccagtag ctgcatggcc tgacgaagtg
       61 aattgatatg ttcgtcccgg gcattcactg catctttcag cccggcgttt tctgcctgca
      121 aaagtgctac ctgatgctgt aaattctgta aaaaatcact gttaacacct gtcgagcggt
      181 cgtcaaattt tacaacagca tggtcacgtt cattgtcaaa agaaagagaa ccaaaaacac
      241 gaataagctc tgtagtatca ataactttta cagctttccc atgctttaca acagaggtgt
      301 aacttaactc accagattta attaacttgt aaatagtcgg acgactgaca caagcaaggc
      361 gtgccgcttc gctaatagat accctggcca ttatagatcc ccctgatgac catccagacg
      421 aatagtcaga gtgcgacaga gtagttccgc atcctcatgg agcttttcgc aaaggtccgc
      481 ctcagcatcg agctcgagtt cattaaattt ttccagcaaa agcagggtct gccccttaat
      541 aaacttcgcc atattaagcg cagttttctg tggtttcgtc atcacagcgt cagtgctcca
      601 tgttaactct ggttcttttc ctcttcctcg accgttcgct cgctacgctc ggtcacttgt
      661 ctgcggcgag cggacggggc ttacggagaa gcaggtaaga gagtagatga tggacgtaag
      721 gaaagggcag ccaaaaagca tgagaaggcc acgccccctg ggcgttttac cataggctcc
      781 gcccccctga cgagcatcac agaatctgac gctcaaatca gtggtggcga aacccgacag
      841 gactataaag ataccaggcg tttccccctg gtggctccct cgtgcgctct cctgttcccg
      901 cctttcggtt taccggtgtc attccgcagt tatggccgcg tttatctcat tccacgcctg
      961 acactcagtt ccgggtaggc agttcgctcc aagctggact gtatgcacga accccccgtt
     1021 cagtccgact gctgcgcctt atccggtaac tatcatcttg agtccaaccc ggaaaggcac
     1081 gacttatcgc cactggcagc agccactagt aactgattta gaggagttag tcttgaagtt
     1141 atgcgccggt taaggctaaa ctggaagaac aagttttggt gactgtgctc ctccaagcca
     1201 gttacctcgg ttcaaaaagc gccaactctt tgaaccctcg aaaaaccgcc cgccaaggcg
     1261 gttttttcgt ttcgatgaag attatccttc aataagctca ctcgtcaaga taacattcca
     1321 cactggggat acattagccg cagaggcaaa gatgaaaatt aaagtagaaa atttaggatt
     1381 tatctcttca ggtgaaatag acataaaaga ccttacgatt atctttggta aaaataacgt
     1441 aggaaaaact tatcttagtt atgccactta cggaatatta agccgattga gtagtttatc
     1501 tgaaggttca actatcgtat caaaatcaga ctttaataaa ctaaaagcag atggctctat
     1561 atcaatcgat acatctaaag ttgcatcgaa agagataatc caaaaagtta ataaagattt
     1621 cacaaagtca ctctcttcat tttttaacgc aaaagaagat agttttaaag atgccaatat
     1681 agaaatagaa ccaaatttca cagatagtga tttattaaaa cttagttttt cttccaattt
     1741 aaatctggat gggacaggag tctactcgtt taataagagt aagaactctt ctgagattgt
     1801 tatttcattt gtaaaactac ctgaagaggc tacaaataag tcggtaggtt ttgcttttgg
     1861 tgaagatacg atagcaagca tactatcatc aataacaagc aacttaattc taaagaacat
     1921 attcaaagga ttgtctaggc ctttcgtaat aacatcagaa agaacaggta tttctttatt
     1981 ttataaggag atggattcgc atagaagttc attacttaat cattggataa cttcaaaatc
     2041 aagcatgtct acgccaataa ataaaaaact atctgcgtac tcaaccccta taagcgataa
     2101 tataaatatc attaggcaat acgaaagcct aaccaaaaga aagagttttt tatattcgaa
     2161 aaggtctaaa agatctaatc gtttaatgac cgagacctta gaaagcatgc tttccggttc
     2221 atttaagcac gccaatggcg aaactatttt cacaaaaaaa gaagatgaca aagatgtaag
     2281 cattccaatg tctatatcgt catcttcagt taaatcattg tttttacttg atttatacat
     2341 aaaacatgtt gctcaatatg gcgatttcct tgtgatcgat gagccagaat taaacttgca
     2401 cccagaaaat caagtgagaa tggctgaatt gatagtaaga ctgataaact tagggataaa
     2461 aataatcatg acaacacata gtgattatat tattaaggaa atcaacaata gaataatgct
     2521 aagcaatatt agcaaaaaag aaaatcttta tgatttatca tttagagatg aagatgtttt
     2581 gcgccaagat agagttagcg catttaccat ttgtgatgac agaaaaataa aagaaataca
     2641 agtagacaag tatgggataa atcaggagat atttgatgat gtaatttcat ctctcaatga
     2701 gagaagtgat cttatatacg acgcactatg tcaggaataa tcggatattg tatatgatta
     2761 gcgcaataaa gaaagttata gacgataggg ttaagataga aataataaaa acggcaaatg
     2821 accatgagct agtgttaaaa gaagaaagtg atggtagtga tattgaagaa ctcaggataa
     2881 taaatgttcc tgaggagtca tttgcattta ccttggatta tacatcaact agtggctccc
     2941 ttaaaaatat tcgtttgttc aaaaaactat cttgttatgt cagttcaaaa aatgaagatg
     3001 ggataaataa atcctgcgat ctggtcatag ttacaaagag agatgacgga gtaaaggttg
     3061 tagttctaga tttaaaatca aaaaggacat ctggaaaaag accaactatt cagatagaaa
     3121 actctatact ttttttaaac tatatttttt ctttgattga tttttattat aaggaagaaa
     3181 ttggaattgc tattgatgat attaaatata taaaggcatt agtcacaaca gggccaactc
     3241 aaaaaacaac tgtgtctaaa agaccgtcaa aatctagtga tgtaaagaaa attcctgtta
     3301 aggcaatgca taaaaaagca acgattcgat atagcagcat agccgcataa acctatggaa
     3361 agtgagggca acctcacttt ccaatcatct tatttaccat aacgtctcat tacgcgtacc
     3421 gctaaaacgc gctgaacgcg attctgccgc aaacaccgca aaaagagatg ctttatccag
     3481 tgaaaaccag aaaaatgcgt caggatcgtt ttcagctcgc tgcatagcta tgcatgagag
     3541 tgaatggcga acggtttggg tgcatacagt gcccatgagg cacattttca gacattttca
     3601 gttcgtgaat tccaagcatt ttttacagga cacccctagc agcgccccta ggggtgtcct
     3661 gtaaaaagat gcgacgcgcc tctagggacg accctacatt aattaactgt tttttataaa
     3721 gattgtcagt actgacccta agtagcgtcg tcatagcatc gccatagggt cgtcaacgac
     3781 gtgcttttgc ataaatctga aaaagaaaat acatttttaa aacaataaca tcatgattta
     3841 aaaagaaaat cagcaaaaag ttagttttgc gtggggtgtg ggcatttcag gcatgagaac
     3901 agactcgcgt ttttacgggg tatctgcgga atttttgatt aaaaaaacat cgacgcagag
     3961 cgaaatttta tgcaacagcg gctgtactgc acagggatta tttatcagtt gatatgctgt
     4021 gtcatgatac tacctgaaga aacaggacag gatgtttaat tgtaataccg gcacacacaa
     4081 cgtattgcca cttggtcaga gtttccccca caacatcagt gcgaacgtgc ttaatgctcg
     4141 ctacggctct ctcatgttgc cggtgattcc gttgttgttc tttcaggaat gagtcatcag
     4201 atagccccag aaactcgctc agaagcactc agacgcgtga aacgggtttt agatgcccgt
     4261 cagggcatgg aaggcgcgaa taacgcttac agagcgtttc aggaggtcag gcgcgccgat
     4321 acctaactag gggatttcat gtcgctggga accgagtcat cccctgcaaa gccaattcgc
     4381 acggaacagt aagccactcg gttggtagat ggtcgtagac cgtcagtgct acagcaatgg
     4441 gggtctcccc agacggtttc ctgttgcgct caaggctctg ccggaaccgt agcggcaagg
     4501 ataaaaaacc ctgcgcaatt cccgcagggg aaggtgaaaa taactaccta tctcttacgt
     4561 ttgagttttg aactcagact gaatatgcat ttgatagtgt tgaatttgca agaatcggcg
     4621 gcgattttac ggtcgacaaa agagcaatgc aggaatatcg actccaactc aatgctctta
     4681 atgtgggaaa atttccgttt tccaaattac cccaaactga gtggcagacc gaacgctatg
     4741 gctgggatgc gtggtaatgg ctcaacggaa tttccaaaac tgccaccagg actttgctcg
     4801 ga
//
