LOCUS       NZ_CP012638             3904 bp    DNA     circular CON 11-JUN-2024
DEFINITION  Escherichia coli strain SF-088 plasmid pSF-088-3, complete sequence.
ACCESSION   NZ_CP012638
VERSION     NZ_CP012638.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN04026225
            Assembly: GCF_001280325.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3904)
  AUTHORS   Stephens,C.M., Skerker,J.M., Sekhon,M.S., Arkin,A.P. and Riley,L.W.
  TITLE     Complete Genome Sequences of Four Escherichia coli ST95 Isolates
            from Bloodstream Infections
  JOURNAL   Genome Announc 3 (6), e01241-15 (2015)
   PUBMED   26543109
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3904)
  AUTHORS   Stephens,C.M., Skerker,J., Sekhon,M., Arkin,A. and Riley,L.W.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-SEP-2015) Biology, Santa Clara University, 500 El
            Camino Real, Santa Clara, CA 95053, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. 3
            Genome Coverage                   :: 90X
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_001280325.1-RS_2024_06_11
            Annotation Date                   :: 06/11/2024 02:33:42
            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)                     :: 5,147
            CDSs (total)                      :: 5,025
            Genes (coding)                    :: 4,786
            CDSs (with protein)               :: 4,786
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 94
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 239
            CDSs (without protein)            :: 239
            Pseudo Genes (ambiguous residues) :: 0 of 239
            Pseudo Genes (frameshifted)       :: 95 of 239
            Pseudo Genes (incomplete)         :: 159 of 239
            Pseudo Genes (internal stop)      :: 40 of 239
            Pseudo Genes (multiple problems)  :: 50 of 239
            Pseudo Genes (short protein)      :: 1 of 239
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP012638.1.
            Source DNA is available from: Craig Stephens, Biology Dept., Santa
            Clara University, Santa Clara, CA, 95053.
            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..3904
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SF-088"
                     /isolation_source="patient blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSF-088-3"
                     /geo_loc_name="USA: San Francisco"
                     /lat_lon="37.755651 N 122.404572 W"
                     /collection_date="2007-09-06"
                     /collected_by="SFGH"
     gene            join(3787..3904,1..902)
                     /locus_tag="AN203_RS26285"
                     /old_locus_tag="AN203_26335"
     CDS             join(3787..3904,1..902)
                     /locus_tag="AN203_RS26285"
                     /old_locus_tag="AN203_26335"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001271373.1"
                     /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_011017196.1"
                     /translation="MSAALQYFEENLPRRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWQVMEWREEAYTLDELADYLDLSASA
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLDAVIQRVEMYNASLPVPLSP
                     PECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGKANSSENQSDKGKKS
                     AAVRWTANDDKRRRALDMYILGASTEDIAVAVGVSSRTIRRWMDNSGEWLTKKQIIKF"
                     /name="replication initiation protein"
     gene            complement(1163..1609)
                     /locus_tag="AN203_RS26290"
                     /old_locus_tag="AN203_26340"
     CDS             complement(1163..1609)
                     /locus_tag="AN203_RS26290"
                     /old_locus_tag="AN203_26340"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000184721.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="conjugal transfer protein TraD"
                     /protein_id="WP_000184723.1"
                     /translation="MTNREEWLSAKIAYINGLKSPSEQQRLLVLLAEKKNRTTTDEKTL
                     SALIRAEKTAEKAAAAKARVTAIIAAERKAAARAERKARDHELYKAAGLMIVAGLVDSK
                     TGKPKFSAAELVGALAGIAELPRNHPKWQEWERRGKELLTKDSA"
                     /name="conjugal transfer protein TraD"
     gene            1781..3331
                     /locus_tag="AN203_RS26295"
                     /old_locus_tag="AN203_26345"
     CDS             1781..3331
                     /locus_tag="AN203_RS26295"
                     /old_locus_tag="AN203_26345"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001624483.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_001624483.1"
                     /translation="MASYHCTVKAGAKGSALKHADYISRSGEYKSYKSREDLEFSSSGN
                     MPSWAKKNPAELWKAADEFERKNGTAYREIEIALPRELTREQRIELVEDFVQKELGDRH
                     AYQYAIHNPPGAIDGKEQPHAHIMFCERINDGIERDPQQFFKRANSKSPERGGAKKASI
                     PQTAGERKAALVALRSRWADVQNEHLARYGHESRVDHRSLKEQGINRTPEVHLGPVQAA
                     SLNGEQIVAIQERRNAERELKTARDAANAIQQEQEQKQKIKAVEPVRSARSPELLLQYR
                     KVMKTVIQGEARLARLGDANPNALKEHKLLQNAKAKKDSLSEWSRRIYEGARYLDKLGR
                     NVVSAQRELRELQEQRNALNGIRGLFRGADKREIDARILEQKSVLETAEHERNEFRNKL
                     QQAESEWDKENAAFKRTEGYKYVGDLDRYREREILAAASLENTRQKVAEEVSVARSQML
                     SLEPELSISGDEKAQMRHELLAEMAQERQQQEEKALRIQRSWAREASRSNERDQDMER"
                     /name="MobA/MobL family protein"
     Typing          2..658
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.544"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          1782..3328
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.629"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tccagcagaa ccagcctcat gcgcagttct ggctggtttt tgacgttgac cgcgaggggg
       61 cagcgattga ctggagcgac cggaacgccc ccgcgccgaa catcaccgtt aaaaatcctg
      121 tgaacggaca cgctcacctg ctctatgcac tcaatatcgc cgtgagaacc gcgcctgatg
      181 cgtcggttaa ggcgctgaaa tatgccgcag cggttgaacg ttcgctgtgt gagaaacttt
      241 gtgctgatgt gaactacagc ggactgattt gcaaaaatcc gttccacctg gaatggcagg
      301 tgatggagtg gcgcgaggaa gcctataccc tcgatgaact ggctgattat ctcgatttga
      361 gcgcctcagc gcgtcgtagc atcgataaac attacgggat ggggcgaaac tgccacctgt
      421 tcgaaatgac gcgcaaatgg gcttacaggg cgattcgtca gggctggcca gcattctcac
      481 agtggcttga tgccgtgatt cagcgtgtcg aaatgtacaa cgcatcgctt cccgttccgc
      541 tttctccgcc tgaatgtcgg gctattggca agagcattgc gaaatacacg cacaggaact
      601 tcacgccgga aactttcgca cagtatgtgg ctgatacgca cacgccagaa attcaggcag
      661 cacgcggtcg caagggcggg aaggccaatt cgtcagaaaa tcagtcggac aaagggaaaa
      721 aaagcgccgc tgttcggtgg actgctaacg acgacaaacg tcgtagggcg cttgatatgt
      781 atatcttggg agcgtcaacg gaagatattg cagtggcggt tggtgttagc agccggacta
      841 ttcgacgctg gatggataat tctggagaat ggttaaccaa gaaacaaata attaaatttt
      901 aattaacaga aaaataacaa ttaccccctg tttttgttaa tggatggtta aattcgcgga
      961 catgaacaag cctatatcag ataacagcgc ctttcggcgt ctttttgagc agcgggcttt
     1021 ccggcggttt tctcctgtca gcccagcaat ggtgcggctt accgcatgat tgaggtggtt
     1081 gtgctcgccg cagtctcatg accgagcgta gcgagcgaat gagcgaggaa gcaccaggga
     1141 aacggaacgt gaacggaggc tcttacgcac tgtctttggt tagtagctcc ttcccgcgtc
     1201 tttcccattc ctgccatttt gggtggttgc gcggtagctc tgcgattcct gcgagtgcgc
     1261 ctaccagttc ggcagcacta aactttggtt ttccggtttt gctgtccacc agtcctgcca
     1321 caatcatgag gcctgcggcc ttgtagagtt catgatcccg cgcctttcgt tccgcccttg
     1381 cggctgcctt ccgttctgcc gctatgattg ccgttaccct ggcttttgct gcggctgctt
     1441 tctctgcggt tttttctgcc cgtatcagtg cggacaacgt tttttcatcc gtcgttgttc
     1501 ggtttttttt ctctgccagt aacacaagta atctctgctg ctctgacggt gatttcagtc
     1561 cgttgatgta ggcaattttt gcacttaacc actcttcacg atttgtcatt cttacctctg
     1621 catttttgcc gttaatgtga gttgttattg tgcataatat caccttgtct gcctgcgtgt
     1681 gagaccgtaa aatcatccct gattaattca gggatgcgca cttagtagtt tctctccttc
     1741 gtcgagaaac tgtgcgctcc tgcggagggc taaaaggcag atggcaagct accattgcac
     1801 cgtcaaagct ggagcaaaag gcagtgcctt aaaacatgct gattacattt ccagatccgg
     1861 cgaatataag agctacaaat cgcgggagga tctggaattt tcgtcatcag gtaacatgcc
     1921 atcatgggcg aagaaaaatc ccgcagagct atggaaagcc gcagatgaat ttgaacgaaa
     1981 aaacgggact gcataccgtg aaattgagat cgcgttaccg cgtgaactga cacgcgaaca
     2041 acggatagaa cttgttgaag atttcgtgca aaaggaactt ggcgatcgcc atgcctacca
     2101 gtacgcgatc cacaatccgc caggtgcaat cgacggaaag gaacagccac acgcgcatat
     2161 catgttttgc gagcggatta atgatggtat tgaacgcgat ccgcagcaat tttttaaacg
     2221 tgccaacagc aaatcaccag aacggggagg cgcaaaaaaa gcgagtattc cccagacagc
     2281 cggagagcga aaagccgccc ttgttgcgct gcgttcccgc tgggcagatg tgcagaatga
     2341 gcaccttgcg cgatacggtc acgagtcgcg cgtagatcat cgttctctga aagaacaggg
     2401 tatcaatcgc acgccggaag ttcatcttgg ccccgttcag gccgccagtc tcaatggtga
     2461 gcagattgtt gcaatccagg aacggaggaa tgccgagcgg gaactcaaga ccgccagaga
     2521 tgccgcaaat gccattcagc aggaacagga gcaaaagcaa aaaatcaagg cagttgagcc
     2581 tgttcgttca gcccgttcac cggagttatt gcttcagtac cgcaaggtta tgaaaacggt
     2641 cattcaggga gaagcaaggc ttgctcgttt aggggatgcc aatcccaatg cgctcaaaga
     2701 acataagctg cttcagaatg cgaaagcaaa aaaagactct ctttccgaat ggagcaggcg
     2761 aatatatgaa ggggcacggt atttagacaa actggggcgt aatgtcgttt ccgcacaaag
     2821 ggagctgcgg gagctacagg aacaacgcaa tgctttgaat gggattcgtg gcctgtttcg
     2881 gggggctgac aaaagggaga ttgatgcgcg tattctggag caaaaaagtg tgctggaaac
     2941 cgctgaacat gaaaggaatg aattcaggaa caagctacag caagccgaat ccgagtggga
     3001 caaagaaaac gctgctttta agcgtaccga gggatataag tacgttgggg atctggacag
     3061 gtacagagaa cgtgagattc tggccgcggc atctttagag aataccaggc aaaaggttgc
     3121 tgaagaagta tccgttgccc gtagccagat gttatctctg gagcctgaac tcagtatatc
     3181 tggagatgaa aaagctcaaa tgcgacatga gttactggca gaaatggcgc aggaacggca
     3241 gcaacaggag gaaaaggcac tgcgtataca gcgatcctgg gccagggagg catcacgtag
     3301 taacgaacgt gatcaagata tggagcgttg aaaatgtagc aatatcggga ctgcgccccg
     3361 aaccccgcca acgtttcacg gaacgcgaaa aaattccgcg tcccgttcac cgttttctga
     3421 tgagaaagtt tgctgttttg acccgttcgc ccttctgaac gctcgaaaca gatcgcgcat
     3481 cgctttcgtg catagttatg caacgttctg aaaacgattc tgacgcgttt ttctggtttg
     3541 gcctggtgtt ttcctgtctt tttgcgtttt ttgcgtcagg aagcgactga gggcgtttta
     3601 cggggtacgt acaacaggag ttatggtaaa tggatcgggt ttgcgggaag actcgacagg
     3661 ttttgtcgtt gggggtagtg taagcgactg aaaaacaaac gcccctgaaa ttcgtgtcta
     3721 tccgccaaga ctgtcacgaa aatacagggg cgatgtcggt cgataacctg gaaggaatcg
     3781 taacacatga gcgccgcgct tcaatacttc gaagaaaatt taccccgccg tccctatcac
     3841 acggatgatc tcgcttttgg tcttcgcatc tccggcaaag ggcgtgcgct gcttgcgcgg
     3901 taca
//
