LOCUS       NZ_CP054348             5213 bp    DNA     circular CON 13-JUN-2023
DEFINITION  Escherichia coli strain SCU-176 plasmid pSCU-176-3, complete
            sequence.
ACCESSION   NZ_CP054348
VERSION     NZ_CP054348.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14943547
            Assembly: GCF_013315675.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5213)
  AUTHORS   Stephens,C., Arismendi,T., Wright,M., Hartman,A., Gonzalez,A.,
            Gill,M., Pandori,M. and Hess,D.
  TITLE     Title: F plasmids are the major carriers of antibiotic resistance
            genes in human-associated commensal E. coli
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5213)
  AUTHORS   Stephens,C., Arismendi,T., Wright,M., Hartman,A., Gonzalez,A.,
            Gill,M., Pandori,M. and Hess,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (18-MAY-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                   :: 100x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/13/2023 03:58:56
            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)                     :: 4,962
            CDSs (total)                      :: 4,848
            Genes (coding)                    :: 4,620
            CDSs (with protein)               :: 4,620
            Genes (RNA)                       :: 114
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 228
            CDSs (without protein)            :: 228
            Pseudo Genes (ambiguous residues) :: 0 of 228
            Pseudo Genes (frameshifted)       :: 88 of 228
            Pseudo Genes (incomplete)         :: 149 of 228
            Pseudo Genes (internal stop)      :: 51 of 228
            Pseudo Genes (multiple problems)  :: 52 of 228
            Pseudo Genes (short protein)      :: 3 of 228
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP054348.1.
            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..5213
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-176"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-176-3"
                     /geo_loc_name="USA: California"
                     /collection_date="2017"
     gene            complement(join(5054..5213,1..32))
                     /locus_tag="HPE52_RS24465"
                     /old_locus_tag="HPE52_24450"
     CDS             complement(join(5054..5213,1..32))
                     /locus_tag="HPE52_RS24465"
                     /old_locus_tag="HPE52_24450"
                     /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_000165988.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDSENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            97..423
                     /locus_tag="HPE52_RS24470"
                     /old_locus_tag="HPE52_24455"
     CDS             97..423
                     /locus_tag="HPE52_RS24470"
                     /old_locus_tag="HPE52_24455"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_174165909.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGXXRLPVPGXLPT
                     LAPPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGT
                     RDDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            632..>1063
                     /locus_tag="HPE52_RS24990"
                     /old_locus_tag="HPE52_24460"
                     /pseudo=""
     CDS             632..>1063
                     /locus_tag="HPE52_RS24990"
                     /old_locus_tag="HPE52_24460"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            1101..1619
                     /locus_tag="HPE52_RS24480"
                     /old_locus_tag="HPE52_24465"
     CDS             1101..1619
                     /locus_tag="HPE52_RS24480"
                     /old_locus_tag="HPE52_24465"
                     /inference="COORDINATES: protein motif:HMM:NF016710.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_023144181.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETILNDEFRKLEKSVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVIFLFTVSC
                     GTLWYLGGMIQANLEDIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVIPHQ
                     GKDWVQLME"
                     /name="MbeB family mobilization protein"
     gene            1626..1859
                     /locus_tag="HPE52_RS24485"
                     /old_locus_tag="HPE52_24470"
     CDS             1626..1859
                     /locus_tag="HPE52_RS24485"
                     /old_locus_tag="HPE52_24470"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_001555310.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWESAFVELQKMFSLTQRDNA
                     MLNERVMKLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2406..2702)
                     /locus_tag="HPE52_RS24490"
                     /old_locus_tag="HPE52_24475"
     CDS             complement(2406..2702)
                     /locus_tag="HPE52_RS24490"
                     /old_locus_tag="HPE52_24475"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001679964.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000047647.1"
                     /translation="MSKTKSGRHRLSKTDKRLLAALIAAGYEERTARDLIQKHVYTLTQ
                     ADLRHLVSEISNGVGQSQAYDAIYQARRIRLARKFLNGKKPEEGLNAWKGDLP"
                     /name="hypothetical protein"
     gene            2914..3111
                     /locus_tag="HPE52_RS24495"
                     /old_locus_tag="HPE52_24480"
     CDS             2914..3111
                     /locus_tag="HPE52_RS24495"
                     /old_locus_tag="HPE52_24480"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335786.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001335786.1"
                     /translation="MKEEKVLLHRFLFVVRNKNGCELSCSADLMGTRDDVYKYFSDSVS
                     GLDVELIDVSCESEWEEHSH"
                     /name="hypothetical protein"
     gene            3129..3413
                     /locus_tag="HPE52_RS24500"
                     /old_locus_tag="HPE52_24485"
     CDS             3129..3413
                     /locus_tag="HPE52_RS24500"
                     /old_locus_tag="HPE52_24485"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000625497.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin Z C-terminal domain-related protein"
                     /protein_id="WP_000625497.1"
                     /translation="MISQNVWAPPFFFGPWVELENHTGDIAYTVYFDTLSNVPGPFIAF
                     IWYAPNGPRTVNVIGPASYQISCKGAGVDKIKFKSVSGTGQIIHVYTTL"
                     /name="colicin Z C-terminal domain-related protein"
     gene            complement(3477..3866)
                     /locus_tag="HPE52_RS24505"
                     /old_locus_tag="HPE52_24490"
     CDS             complement(3477..3866)
                     /locus_tag="HPE52_RS24505"
                     /old_locus_tag="HPE52_24490"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001679965.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000477210.1"
                     /translation="MFKSSVKSITSSTILTLLIGCSSTETNKNIVYKVGGDSIILNKYC
                     ILKMYPSQSEKNKGVIIEVNTDSLCKKKLNEITSKNIGKPLISYFDGKVISQPAIIHSA
                     LNPTHYYQPVNDETTVMEIIKAYSK"
                     /name="hypothetical protein"
     Typing          4882..4969
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.86e-39"
     Typing          complement(4315..4871)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          414..1963
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.555"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgttaaggg cggttttttc ctgtttagtc actgatgcct ccgtgtaagg gggatttctg
       61 ttcatggggg taatgatacc gatgaaacgc gagaggatgc tcacgatacg ggttactgat
      121 gatgaacatg cccggttact ggaacgctgt gagggtaaac aactggcggt atggatgcgg
      181 cgggtctgcc tgggnntgrg ccggttgccc gttccgggnr ggctgccgac actggcaccg
      241 ccgttactgc gtcagctggc agccatcggg aataacctga accagacagc ccgtaaggtg
      301 aacagcggac agtggtcttc cggcgaccgg gttcaggtgg tggccgcact gatggccatc
      361 ggggatgagc tgcgccggtt gcgtctggcc gtcagggaac aggggacgcg ggatgatagt
      421 taagtttcat gcccggggaa aaggtggtgg cagtggtccg gttgattacc tgctgggaag
      481 ggagcgtaac cgggaagggg caacggtgct tcagggtaat ccggaagaag tacgggaact
      541 catcgatgcc acgccatttg cgaagaaata cacgtccggt gtgctgtcgt tcgcggagaa
      601 ggagctgcca ccgggaggac gtgaaaaggt gatggcgagc tttgagcgtg tactgatgcc
      661 cggtctcgaa aaaaatcagt acagcatcct gtgggtggag caccaggaca agggacggct
      721 tgagctgaat tttgtcattc cgaacatgga gctacagacc ggaaaacgcc tccagccgta
      781 ctacgaccgg gcagacaggc cgagaattga tgcctggcag acgctggtga atcaccatta
      841 cgggctgcat gaccccaacg ccccggagaa ccgccggata ctgactctct ctgataacct
      901 gccggaaacg aaacaggcgc ttgcagagag cgtcacacgc gggatagacg ctctttatca
      961 tgtcggggag ataaaaggcc gtcaggatgt gattcaggcg ctcacagagg cagggcttga
     1021 agtggtcagg gtgacgcgaa gcagtatcag cattgcagac ccgaacggtg ggaagaatat
     1081 caggctgaaa ggagcatttt atgagcaatc ttttacagac gggcgcggag ttcgagaaaa
     1141 agctgaaaga gagagccgaa tctacagaga caatactgaa cgacgagttc aggaagctcg
     1201 aaaaatctgt aagcaaggct gtgacatcaa acgagacgaa aatcaaagac gctatagccc
     1261 tgttcacagc ttcgacagag gaatcactga aaaagcaccg ggaaggggtg aaagaggcga
     1321 tgatgcagca caggaaggac gtgttaaagc tggcagggaa tacgggcatg atgttactgg
     1381 ggatggtcat tttcctgttt accgtgagtt gcgggacgct ctggtatctt ggcgggatga
     1441 tacaggcgaa cctggaagat atcaggaagc aggaagagac attgcagaaa ctgaacgcga
     1501 agacatgggg cgtggagttc gtacaggacg ggaacaggaa atttctggtc cttccgtacg
     1561 ggaaatcagc agaggtgatt ccccatcagg ggaaggactg ggtacaactg atggagtgac
     1621 acagagtgac ggagctggaa agacatttgc tgaacgcatt agagcaactg caacaggact
     1681 atatgcagcg gctgaacgaa tgggagagcg ccttcgtgga attgcagaaa atgttttcgc
     1741 ttacgcaacg ggacaacgcg atgctgaacg agcgggtcat gaagttgagt cagcaggtgc
     1801 agcacttgag cgagcggaca gaacgcttga gccagttata cagcgagaac aggagataag
     1861 ggacgaacgg ctgatacagg aacgcgaaca tgagttatcc ctggagcgtg agcgccagct
     1921 ggaaatacag gaacggacac tggatggccc ttcgctggga tggtaatcag agacaggcta
     1981 aaatgttgtc agcgcgtttc cggtgcattt tttgggataa tggttggttc ggggcaccgg
     2041 gaacgcgctt cagtcataaa ccttgctgaa aacacaggaa cgcgttaaaa cgcatacggg
     2101 cgcgattctg gtgtgtcttt catagtcgtg tttttgcctc tattgccaga tcgcgctcat
     2161 tcccctgaac ttctgttttc ctgctcaaat ccccgtcttc ttcgcttccg aaagtatgaa
     2221 aaaaatccgt ttcagcggtc tctgactggc aattcctgcg tgattcacct ggctgcatag
     2281 gtatgcatgt ggttaaaatt taccgggtgc gatcgcggca gttttccggg tggtttgttg
     2341 ccatttttac ctgtctgctg ccgtgatcgc accgaacgcg tttcggcggt gcgtacaata
     2401 agtgattatg gtaaatcacc cttccaggcg ttcagccctt cttccggttt ttttccgttc
     2461 aggaatttac gggcgagacg aatgcgtctt gcctggtaaa tcgcatcgta ggcctgtgac
     2521 tgtcccacac cgttactgat ttcactgacc agatggcgca ggtcggcctg tgtcagtgtg
     2581 taaacgtgtt tctggatgag gtcacgggct gtccgctctt cgtatccggc agcgataagt
     2641 gcagccagca ggcgtttgtc tgttttgctc agtcggtggc gaccagattt tgttttgctc
     2701 acgttatctc ctctctgttt tttctcctga tgttatccgg tgctgttttt ctgctgcgaa
     2761 tcttcccttc ctgattttta taagggtgat tcagatcaca aaaatgaaaa ttcatatcat
     2821 tgacaggaaa aataatgcgg cgtaatttat actgtatata aaactagtat ttatatatac
     2881 agtatattct gtgtaaataa agggagggat aaaatgaaag aagaaaaagt attgcttcac
     2941 cgtttcttat ttgtagttag gaataagaat ggttgtgaac tatcatgttc ggcagacctt
     3001 atgggaacaa gggatgatgt ttataagtat ttctctgatt ctgttagtgg gctagatgtt
     3061 gagcttatag atgtttcttg cgagagtgaa tgggaagaac attcgcattg aactaatcag
     3121 gagattatat gatttctcaa aatgtttggg ctcctccttt cttttttggt ccttgggttg
     3181 aacttgaaaa tcatactggt gatatcgcgt acactgtcta ttttgataca ttgtctaatg
     3241 tacccggtcc atttattgct tttatctggt atgcccctaa tgggccaaga acagttaacg
     3301 ttattggtcc agcatcttat cagatctctt gcaagggcgc tggtgttgat aaaattaaat
     3361 ttaaaagtgt cagtgggaca gggcagatta ttcatgtata cactacctta taataagagc
     3421 tgaataaata taatcctgcc taagctatac cttaagcagg attatatcta ttaatattat
     3481 tttgaatatg cttttatgat ttccatcact gttgtttcat cgttcacagg ttgataataa
     3541 tgggttggat ttagtgcaga atgaatgatt gcaggttggg atattacttt tccatcaaaa
     3601 tatgaaatca ggggtttccc tatattttta ctagttattt cgtttagttt tttcttacat
     3661 aaactatctg tgtttacttc tattatgacg cctttgtttt tttctgattg ggaagggtac
     3721 attttaagta tgcaatattt attcagaatg atgctgtcac caccaacttt gtaaacaatg
     3781 tttttgtttg tttcagtact tgaacatcct ataagtaagg tcagtatagt actcgatgtt
     3841 attgacttta ctgatgattt gaacatatta actccatttt attttgttaa aattccaatc
     3901 tataaataca tatacacgta aaaataaaca atgcgaacgt tttcacttat attatcccca
     3961 tgatgtgatt gaatggtggt tccatataag agagggcaat tatactatct ttctctcctg
     4021 aactgatggg attgcagttt agagaaaaaa agatcaaagg atcttcttga gatccttttt
     4081 ttctgcgcgt aatctgctgc ctgtaaacga aaaaaccacc ctggcaggtg gtttttcgaa
     4141 ggttagctaa tcctggcaga ttacctaacc gggtagctgg cttaagtgga gcacagatac
     4201 caaaagatgt cctttcagtg tagccgctat aaggcttcaa cttcaagagt tctgcgtatc
     4261 taaatccact ttttagttac caatggctgc tgccagtggc gttaagtcgt gtcttaccgg
     4321 gttggactca agacgatagt taccggataa ggcgcagcgg tcgggctgaa cggggggttc
     4381 gtgcacacag cccagcttgg agcgaacgac ctacaccgaa ctgagatacc tacagcgtga
     4441 gctatgagaa agcgccacgc ttcccgaagg gagaaaggcg gacaggtatc cggtaaacgg
     4501 taaggtcgga acaggagagc gcacgaggga gcttccgggg ggaaacgcct ggtatcttta
     4561 agtcctgtcg ggtttcgcca cctctgactt gagcgtcgat ttttgtgatg ctcgtcaggg
     4621 gggcggagcc tatggaaaaa cgccagcggc gcggccttct tcctgttcct ggtcttttgc
     4681 tcacatgttt tttccggtgt tatcccctga ttctgtggat aacagcattt cgtttttgag
     4741 tgagtagata ccgctcgccg cagccgaacg accgagcgta gcgagtcagt gagcgaggaa
     4801 gcggaaaagc gcctggacgt gcattttctc cttacgcatc tgtgcggcat ttcacacccg
     4861 gtatggcgca cgtttcatac aatccgcact gatgccgcat ggttaagcca gtatacactc
     4921 cgctatcgct acgtgactgg ttcagggctg cgccccgaaa cccgctaaaa caccctgacg
     4981 cgccctggcg ggcttgtctg ctcccggcat ccgctcacag gcaagctgtg accgtctccg
     5041 ggagctgcat atgtcagagg ttttcactgt catccccgaa gcgcgcgagg cagctgcggt
     5101 aaagctcatc ggcgtggtcg tgaagcgatt cacagatatc tgcctgttca tccgcgtcca
     5161 gttcgttgag cttctccagc agcgttaatg tctggcttct gataaagcgg gcc
//
