LOCUS       NZ_CP051752             5892 bp    DNA     linear   CON 26-JUN-2024
DEFINITION  Escherichia coli strain SCU-301 plasmid pSCU-301-1, complete
            sequence.
ACCESSION   NZ_CP051752
VERSION     NZ_CP051752.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14609790
            Assembly: GCF_012934695.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5892)
  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  JOURNAL   Unpublished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 5892)
  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                   :: 20x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_012934695.1-RS_2024_06_26
            Annotation Date                   :: 06/26/2024 01:47:32
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,841
            CDSs (total)                      :: 4,728
            Genes (coding)                    :: 4,560
            CDSs (with protein)               :: 4,560
            Genes (RNA)                       :: 113
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 168
            CDSs (without protein)            :: 168
            Pseudo Genes (ambiguous residues) :: 0 of 168
            Pseudo Genes (frameshifted)       :: 105 of 168
            Pseudo Genes (incomplete)         :: 76 of 168
            Pseudo Genes (internal stop)      :: 33 of 168
            Pseudo Genes (multiple problems)  :: 37 of 168
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP051752.1.
            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..5892
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-301"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-301-1"
                     /geo_loc_name="USA: California"
     gene            complement(<1..463)
                     /locus_tag="HHJ43_RS24495"
     CDS             complement(<1..463)
                     /locus_tag="HHJ43_RS24495"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001525988.1"
                     /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_250854608.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLGESVSEAVTSNE
                     TKIRDAIALFTVSTEKSLEKHREGVKEAMMQHRKDVLKLAGNTGMMLLGIVFLLFTASG
                     GTLWYLGGRIQTNLEEIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYG"
                     /name="MbeB family mobilization protein"
     gene            complement(<501..1151)
                     /locus_tag="HHJ43_RS24500"
                     /pseudo=""
     CDS             complement(<501..1151)
                     /locus_tag="HHJ43_RS24500"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /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            complement(1141..1464)
                     /locus_tag="HHJ43_RS24035"
                     /old_locus_tag="HHJ43_24045"
     CDS             complement(1141..1464)
                     /locus_tag="HHJ43_RS24035"
                     /old_locus_tag="HHJ43_24045"
                     /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_024242645.1"
                     /translation="MLTIRVTDDEHARLLERCDGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1529..1720
                     /locus_tag="HHJ43_RS24040"
                     /old_locus_tag="HHJ43_24050"
     CDS             1529..1720
                     /locus_tag="HHJ43_RS24040"
                     /old_locus_tag="HHJ43_24050"
                     /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_000165993.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHEHA
                     DELYRSCLSRFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2391..2549
                     /locus_tag="HHJ43_RS24660"
     CDS             2391..2549
                     /locus_tag="HHJ43_RS24660"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_071529495.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDKAPLAAATGNWTRWIEIL
                     RVLEVVA"
                     /name="replication initiation protein"
     gene            2868..3680
                     /locus_tag="HHJ43_RS24050"
                     /old_locus_tag="HHJ43_24060"
     CDS             2868..3680
                     /locus_tag="HHJ43_RS24050"
                     /old_locus_tag="HHJ43_24060"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000549943.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EcsC family protein"
                     /protein_id="WP_000549944.1"
                     /translation="MHLEEGDLRALERAVELLEQDTITETLTQLVGTPIDYLMSKLPKG
                     AEEQIYSLVEKSLHKAADAALWSLDNEPNRIASTKTNKFFAAVSGAIGGAFGFSALAIE
                     LPVSTTIMLRSIADIARSEGFELDNIDTKLACLEVFSLGGPSDDDDAANTAYYATRSLT
                     AEIVQDLSKEISNIAVKNASSVQTGKWLASLIEKVATRFGIVITEKMAAQVVPVIGALT
                     GATLNTMFTDYYQDMARGHFIVKRLEKKYGNELIKAEYIKISSKLTNS"
                     /name="EcsC family protein"
     gene            3908..4342
                     /locus_tag="HHJ43_RS24055"
                     /old_locus_tag="HHJ43_24065"
     CDS             3908..4342
                     /locus_tag="HHJ43_RS24055"
                     /old_locus_tag="HHJ43_24065"
                     /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_021551691.1"
                     /translation="MGFWDSIKNAAIKAKCGVGIHGGNYKLIDGETCKYSKLCPDCNRT
                     IQKEQHKYGEESYKYDFKCTTVKKCIDCGAEQEGERHERFVEIAVDDYCNVKERCVRCF
                     TERVHGKRHNWYLSGSSDTYRHYKCSVCGEEKEERKTSFR"
                     /name="hypothetical protein"
     gene            4378..5262
                     /locus_tag="HHJ43_RS24060"
                     /old_locus_tag="HHJ43_24070"
     CDS             4378..5262
                     /locus_tag="HHJ43_RS24060"
                     /old_locus_tag="HHJ43_24070"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001439342.1"
                     /GO_function="GO:0005525 - GTP binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="GTPase"
                     /protein_id="WP_021551692.1"
                     /translation="MENNTQGIKLIKEAVDVLPKEIRKSVYNKIRNVINYEPVIGIMGK
                     TGAGKSSLCNSIFKGNVCAVSDVEACTRKVQELIISFGDRTIKIIDIPGVGENEAKDIE
                     YEELYKNLLPELDLVLWVVKGDDRAFSADEHFYKNVLKPVGGDEKVLFVLNQVDKIEPF
                     REWDEEKHQPSPSQQINIRKKEEYLIERFGFTKHPVISVSANEGYNISRLVEAIVRSLP
                     KEAQSGVVHQVKDEIKTKEIVETAKDGFADTVDRAIDDIIDTVLPKPIASVAKVAKKAI
                     VSVAKSVWGLLFG"
                     /name="GTPase"
     gene            complement(5405..5566)
                     /locus_tag="HHJ43_RS24665"
     CDS             complement(5405..5566)
                     /locus_tag="HHJ43_RS24665"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001405928.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="mobilization protein"
                     /protein_id="WP_071779130.1"
                     /translation="MRYPWNGSVSWKYRNAHWMALRWDGETMKNGRFIGLRRTNVLCAI
                     WLHRYSYG"
                     /name="mobilization protein"
     gene            complement(5597..5830)
                     /locus_tag="HHJ43_RS24065"
                     /old_locus_tag="HHJ43_24075"
     CDS             complement(5597..5830)
                     /locus_tag="HHJ43_RS24065"
                     /old_locus_tag="HHJ43_24075"
                     /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_000137445.1"
                     /translation="MTELETHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          complement(1810..1894)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.674"
                     /coverage="99.0"
                     /evalue="2.36e-33"
     Typing          1914..2463
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.203"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(4..1151)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.778"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(5494..5891)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.429"
                     /coverage="99.0"
                     /evalue="2.2e-46"
ORIGIN
        1 tcccgtacgg aaggaccaga aatttcctgt tcccgtcctg cacaaactcc acgccccatg
       61 tcttcgcgtt cagtttctgc aatgtctctt cctgcttcct gatttcttcc aggttcgtct
      121 gtatccgtcc gccaagatac cagagcgtcc cgccactcgc ggtaaacaga agaaagacta
      181 tccccagtaa catcatgccc gtattccctg ccagctttaa cacgtccttc ctgtgctgca
      241 tcatcgcctc tttcacccct tcccggtgtt tttccagcga tttctctgtc gagactgtga
      301 acagggctat agcgtctctg attttcgtct cgtttgatgt cacagcctcg ctgacagact
      361 cgccgagctt cctgaactcg tcgttcagca ttttctctgt agattcggct ctctctttca
      421 gctttttctc gaactccgcg cccgtctgta aaagattgct cataaaatgc tcctttcagc
      481 ctgatattcc ttccgccgtt cgggtctgca atgctgatac tgcttcgcgt caccctgaca
      541 acctcaactc ccacatctgt gagtgcctga atcacatcct gacggtcttt tatctctccg
      601 gcacggtaaa gcacatcaag cccccgtgta acgctctcag caatcgcctg tttcgtttcc
      661 ggcaggttat cagggagtgt cagcgtcctg cggttctccg gggcattcgg gtcatgcagc
      721 ccgtaatggt gattcaccag cgtctgccag gcatcaattc tcggcctgtc tgcgcggtca
      781 tagtacggct ggaggcgttt tccgctctgt agctccatgt tcggaatgac aaaattcagc
      841 tcaagccgtc ccttgtcctg gtgctcaacc cacaggatgc tgtactgatt tttttcgaga
      901 ccgggcatca gtacacgctc aaagctcgcc atcacttttt cacgtcctcc cggcggcagc
      961 tccttctccg cgaacgacag aacacctgac gtgtatttct tcgcaaatgg cgtggcatcg
     1021 atgagttccc ggacttcttc cggattaccc tgaagcaccg ttgccccttc ccggttacgc
     1081 tcccttccca gcaggtaatc aaccggacca ctgccaccgc cttttcccct ggcatgaaat
     1141 ttaactatca tcccgcgctc cctgttccct gacgacctgc cgtaagctgc gcaactctct
     1201 ctcgatggcc atcagtgcgg ccaccacctg aacccggtca ccggaagacc actgcccgct
     1261 gttcaccttc ctcgccgtct gattcaggtt attcccgatg gcagccagct gacgcagtaa
     1321 cggcggtgcc agtgtcggca gcttcccgga acgggcaacc ggctcaccca ggcatacccg
     1381 ccgcatccat accgccagtt gtttaccatc acagcgttcc agtaaccggg catgttcatc
     1441 atcagtaacc cgtatggtga gcatcctctc gcgtttcatc ggtatcatta ccccataaaa
     1501 cagaaatccc ccttacacgg aggcatcagt gactaaacag gaaaaaaccg cccttaacat
     1561 ggcccgcttt atcagaagcc agacattaac gctactggag aagctcaacg aactggacgc
     1621 ggatgaacag gcagacatct gtgaatctct tcacgagcac gccgatgagc tttaccgcag
     1681 ctgcctctca cgcttcgggg atgacggtga aaacctgtaa cacatgtagc tcccggagac
     1741 ggtcacagct tgccggtgag cggatgccgg gagcagacaa gcccgtcagg gcgcgtcagc
     1801 gggtttttgc gggtgtcggg gcgcagccat gacccagtca cgtagcgata gcggagtgta
     1861 tactggctta actatgcggc atttagtgcg gattgtaaga aaacagcgcc atatacgatg
     1921 tgaaataccg cacagatgcg taaggagaaa ataccgcatc aggcgctctt ccgcttcctc
     1981 gctcactgac tcgctacgct cggtcgttcg gctgcggcga gcggtgccgg ctcactcaaa
     2041 ggcggtaata cggttatcca cagaatcagg ggataaggcc ggaaagaaca tgtgagcaaa
     2101 aaggcaaagg gcaacgaaag gccgcgccgt tggcgttttt ccataggctc cgcccccctg
     2161 acgagcatca caaaaatcga cgctcaagtc agaggtggcg aaacccgaca ggactataaa
     2221 gataccaggc gtttccccct ggtggctccc tcgtgcgctc tcctgttccg accctgccgt
     2281 ttaccggata cctgtccgcc tttctccctt cgggaagcgt agcgctttct catagctcac
     2341 gctgttggta tctcggcccg gtgtaggtcg ttcgctccaa gctgggctgt gtgcacgaac
     2401 cccccgttca gcccgaccgc tgcgccttat ccggtaacta tcgtcttgag tccaacccgg
     2461 taagacacga caaagcgcca ctggcagcag ccactggtaa ctggacaagg tggattgaga
     2521 tattaagagt tcttgaagtg gtggcctaac tgcggctaca ctagaaggac agtatttggt
     2581 atctgtgctc caccaagcca gttaccttcg gaaaaagagt tggtagctct tgatccggca
     2641 aacaaaccac cgttggtagc ggtggttttt ttgtttacag gcagcagatt acgcgcagaa
     2701 aaaaaggatc acaagaggat cctttgatct tttcatcact cctgcttcac agacaacaat
     2761 gatgtcggca tctcgcctat tgaatcactg aactcgctca aggtaagctc ccaagacgaa
     2821 tcacttacaa aagtagacta tcgattgatt cataaaggat tcattatatg catcttgaag
     2881 aaggagatct gcgggcttta gaaagggccg tagaattatt agaacaagat acaattactg
     2941 aaacattaac ccaattagtt ggaaccccaa tagattactt aatgagtaaa cttcccaaag
     3001 gggcagaaga gcaaatttat agtctagtag aaaaatcgct ccacaaagct gctgatgcgg
     3061 ccttatggag tctagacaat gaacctaacc gaatagcatc aactaagaca aataaattct
     3121 ttgcggccgt atctggagcc attggtggcg cttttggctt ttctgcatta gcaattgagt
     3181 taccggtttc aacgacaatt atgcttcgtt caattgctga catagcaaga agtgaaggtt
     3241 ttgagctaga taatattgat accaaactgg cctgcttaga ggtgttttcc ttgggaggac
     3301 catctgatga cgatgatgca gctaatactg catactatgc aacaagaagt ttgactgccg
     3361 agatcgtaca agatttatcc aaagaaattt ctaacattgc tgtcaaaaac gcatcttcag
     3421 tacaaacagg aaaatggtta gcttcgttaa tagaaaaagt tgcaacaaga tttggtatag
     3481 ttattacgga aaaaatggct gctcaagtcg ttcccgttat tggagcacta actggagcca
     3541 cattaaacac aatgtttacc gactattatc aagatatggc tcgaggtcat ttcattgtta
     3601 aaagactcga gaaaaaatat ggcaatgagt taataaaggc tgaatatata aaaatctcaa
     3661 gcaaactcac aaattcgtaa aatatttatc ttggatgaat tagacaatga ctttccaata
     3721 ctatctttgc gggaaaaaca cgaagtttat ccagtgcccc cactttttca gcgctatatt
     3781 taacataaca aaaacattat acagagcata aatccatact catttttata tatccacaca
     3841 ctatacgtgt ataatcgtgt cgatgaattg ttcaacttat atcaactaat cgtagggaga
     3901 tttttccatg ggcttttggg atagcataaa aaatgcagca atcaaggcta agtgtggggt
     3961 aggtatacac ggaggaaact ataagcttat tgatggtgag acttgtaaat attctaaact
     4021 atgccctgac tgcaatcgca ctatacaaaa agaacagcat aaatacggag aggaaagtta
     4081 taaatacgat ttcaagtgca caactgtaaa aaagtgtatc gactgtggcg ctgaacaaga
     4141 aggcgaaagg catgaaagat ttgttgaaat tgcagtcgat gattattgca atgtgaaaga
     4201 aagatgcgtg agatgtttta cagagcgagt tcatggtaaa agacacaatt ggtatcttag
     4261 tgggagttct gatacctatc gccattacaa atgttctgta tgcggggaag aaaaagaaga
     4321 aagaaaaaca agcttccgtt aattcatatg aacaacaaaa tgaggaaaat agtaactatg
     4381 gaaaacaata cgcaaggtat aaaattaatc aaagaagctg tggatgttct acctaaagag
     4441 attcgcaagt ctgtctataa caaaattaga aatgttatta attacgaacc agtaataggg
     4501 attatgggta aaaccggcgc tggtaaatcc agcctatgta attctatctt taaaggtaat
     4561 gtatgtgcag tgagtgatgt agaagcatgc acgagaaagg ttcaggaatt aataatttca
     4621 tttggtgata gaacaattaa aataatagat ataccaggtg taggtgaaaa tgaagctaaa
     4681 gatatagaat atgaagagtt gtataaaaat cttctcccag aattagatct ggtgctttgg
     4741 gttgttaaag gtgatgatcg agcattttca gctgatgagc acttttataa aaatgtttta
     4801 aaaccagttg gtggtgatga aaaagtgttg tttgttttaa accaagtcga caagattgag
     4861 ccattccgcg aatgggatga agaaaaacac caaccatcac cctcacaaca aataaatatt
     4921 agaaaaaagg aagaatactt aatagaacga ttcggtttta ccaaacatcc cgttatatct
     4981 gtatctgcga atgaaggtta taacatttca aggttagtgg aggcaatagt aagatcgctc
     5041 ccaaaggaag cacagagcgg agtggtgcat caagtaaaag acgaaataaa aacaaaagaa
     5101 attgtagaaa cggcaaagga cgggttcgca gacaccgtag atagagctat tgatgatata
     5161 atagacaccg tactacctaa accaatagcg tcagtggcta aagtcgccaa gaaagccatt
     5221 gtttctgtag ctaaaagtgt ttggggattg ctcttcggat aatcaagcag gaaagcccat
     5281 cagtatttaa cataacaaca gtttgtacgt accgctaaaa cgcgttcagc gcgatcacgg
     5341 cagcagacag gtaaaaatag caacaaacca cccgaaaaac tgccacgatc gcgcctgata
     5401 aattttaacc gtatgaatac ctatgcaacc agatggcaca gagcacatta gtccgcctta
     5461 atccaatgaa cctgccattt ttcatggttt caccatccca gcgaagggcc atccagtgtg
     5521 cgttcctgta tttccagctg acgctcccgt tccagggata acgcatgttc gcgctcctgc
     5581 atcaaccgtt cctctcttat ctccagttct cgctgtataa ctggctcaag cgttctgtct
     5641 gctcgctcaa gtgctgcacc tgctgactca actgcatgac ccgctcgttc agcatcgcgt
     5701 tgtcccgttg cgtaagcgaa aacatcttct gcaattccac gaaggcgctc tcccattcgc
     5761 tcagccgctg catatagtcc tgttgcagct gctctaaggc gttcagcaaa tgtgtttcca
     5821 gctctgtcac tctgtgtcac tccttcagat gtacccactc tttcccctga aagggaatca
     5881 tctctgctga tt
//
