LOCUS       NZ_CP054163             2519 bp    DNA     circular CON 10-DEC-2023
DEFINITION  Escherichia coli strain STO_Bone2 plasmid pBone2_4, complete
            sequence.
ACCESSION   NZ_CP054163
VERSION     NZ_CP054163.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15006795
            Assembly: GCF_021498145.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2519)
  AUTHORS   Li,F., Luthje,P., Shafeeq,S., Ahl,M., Akerlund,B. and Romling,U.
  TITLE     Characterization of Escherichia coli isolates from a chronic bone
            infection
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2519)
  AUTHORS   Li,F., Luthje,P., Shafeeq,S. and Romling,U.
  TITLE     Direct Submission
  JOURNAL   Submitted (24-MAY-2020) Department of Microbiology, Tumor and Cell
            Biology, Karolinska Institutet, Solna vagen 9, Stockholm 17165,
            Sweden
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. 3
            Genome Representation             :: Full
            Expected Final Version            :: No
            Genome Coverage                   :: 1043x
            Sequencing Technology             :: PacBio RSII
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/10/2023 02:37:15
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,145
            CDSs (total)                      :: 5,018
            Genes (coding)                    :: 4,804
            CDSs (with protein)               :: 4,804
            Genes (RNA)                       :: 127
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 214
            CDSs (without protein)            :: 214
            Pseudo Genes (ambiguous residues) :: 0 of 214
            Pseudo Genes (frameshifted)       :: 82 of 214
            Pseudo Genes (incomplete)         :: 133 of 214
            Pseudo Genes (internal stop)      :: 52 of 214
            Pseudo Genes (multiple problems)  :: 47 of 214
            Pseudo Genes (short protein)      :: 4 of 214
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP054163.1.
            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..2519
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="STO_Bone2"
                     /isolation_source="bone infection of foot"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pBone2_4"
                     /geo_loc_name="Sweden: Stockholm"
                     /lat_lon="59.351331 N 18.026000 E"
                     /collection_date="2005-01-01"
                     /collected_by="Karolinska University Hospital"
     gene            join(2372..2519,1..>2)
                     /locus_tag="HRS05_RS25185"
                     /pseudo=""
     CDS             join(2372..2519,1..>2)
                     /locus_tag="HRS05_RS25185"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012421200.1"
                     /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="Replication protein"
                     /name="Replication protein"
     gene            271..1236
                     /locus_tag="HRS05_RS25190"
                     /old_locus_tag="HRS05_25065"
     CDS             271..1236
                     /locus_tag="HRS05_RS25190"
                     /old_locus_tag="HRS05_25065"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012421200.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_001287824.1"
                     /translation="MSEDKFLSDYSPRDAVWDTQRTLTDSVGGIYQTAAEFERYALRMA
                     SCSGLLRFGWSTIMETGETRLRLRSAQFCRVRHCPVCQWRRTLMWQARFYQALPKIVVD
                     YPSSRWLFLTLTVRNCEIGELGTVLTAMNAAFKRMEKRKELSPVQGWIRATEVTRGKDG
                     SAHPHFHCLLMVQPSWFKGKNYVKHERWVELWRDCLRVNYEPNIDIRAVKTKTGEVVAN
                     VAEQLQSAVAETLKYSVKPEDMANDPEWFLELTRQLHKRRFISTGGALKNVLQLDRETN
                     EDLVIADDVGDGTDDGKRTAFVWDSGKRRYKRAPEKDKSD"
                     /name="protein rep"
     gene            1240..1506
                     /locus_tag="HRS05_RS25195"
                     /old_locus_tag="HRS05_25070"
     CDS             1240..1506
                     /locus_tag="HRS05_RS25195"
                     /old_locus_tag="HRS05_25070"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001024536.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001024536.1"
                     /translation="MNINIEYLNGNKTIGLFFLRSEAVIPDRFKNLILLIDGLSFGTFG
                     FHPHEGFEDELILYIQKTNERVKTLFVKIDLNGIKFGFLRTHS"
                     /name="hypothetical protein"
     Typing          665..896
                     /name="Col(BS512)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.05e-118"
ORIGIN
        1 tgtatttata cttaagggat aaatggcgga tatgaaatag tggtttagcc cagtaatgac
       61 gaggctttga gtgggttttg acaggtcaaa gaaaatggag cagaattgag gcgtttttaa
      121 tcggcgttgg ggagtgcgtc aacactcccc aacatttcga atgtgtcacc tcagcggcaa
      181 actctggtga catgtactgg ctcgcaatgc acaggtacgt gatgaatata ccacatcaaa
      241 tcacagcctg cccagatcgg agcaggctta atgtcagaag ataaattcct ttcggactac
      301 agcccccgtg atgcagtttg ggatacccag cgcacgctta ccgattctgt cgggggtatc
      361 taccagactg ctgctgaatt cgagcgctat gcactccgta tggcctcctg tagcggtttg
      421 ttacgttttg gttggtctac catcatggaa accggagaaa cgcgcctacg gcttcgtagt
      481 gcgcaatttt gccgtgtccg tcattgccct gtctgccagt ggagaagaac cctcatgtgg
      541 caagcccgtt tttatcaggc tctaccgaaa atcgttgtgg attacccgtc ttcccgatgg
      601 ttgtttctga cgttaactgt caggaactgc gagataggtg aacttggaac agtccttaca
      661 gcaatgaatg cggcgtttaa gcgaatggaa aagcgaaagg agctatcacc tgttcagggg
      721 tggatcaggg ctacggaggt gacgcgaggt aaggatggca gcgcacatcc gcattttcac
      781 tgtctgctga tggtgcaacc ttcttggttt aaagggaaga actacgttaa gcacgaacgt
      841 tgggtagaac tctggcgcga ttgcttgcgg gtgaactatg agccgaatat cgatattcgg
      901 gcagtaaaaa ctaagacagg tgaggttgtg gccaacgttg ccgagcaact gcaaagcgcg
      961 gttgctgaaa cgctgaaata ctccgttaaa ccggaagata tggcaaacga tcctgagtgg
     1021 tttcttgagc tgacgcggca gcttcacaag cgccgtttta tctcgaccgg tggggcgcta
     1081 aaaaacgtcc tccagttgga tcgagaaacc aatgaggatc ttgtcattgc cgacgatgta
     1141 ggggatggca ctgatgacgg gaagcggacg gcgtttgtct gggattcagg taaacggcgt
     1201 tacaaacgcg cccctgagaa ggataaatcg gattaacgta tgaatattaa tattgaatac
     1261 ctgaatggaa ataagactat tggtttattt tttttaagaa gtgaagcggt gattcctgac
     1321 aggtttaaaa accttatttt gcttattgat ggattaagtt ttggcacatt tggttttcat
     1381 ccgcacgaag gttttgagga tgaattaatt ttatatattc agaaaacaaa cgagagggta
     1441 aaaactcttt ttgtgaaaat agatttaaac ggtatcaagt ttggattttt aagaacgcat
     1501 tcttagttct ggaaaagagc cagcggcagg ctgaggtgat aggtacgaga ttgcatgcaa
     1561 tctctagtgc tctgtctatc ctgcattatc ctcagcatta tcctcagcat tatcctcagc
     1621 cttgccaact cgacaccaat gcaggataga caatccgatg tcaaatgtta acactctgcg
     1681 agtggtacat tttccccgga ttatcgtcct gagcctgccg ctggctctct ttctaccgcc
     1741 tcgctttgct cgttgctcaa cgcctcacag acacggatta aaatccgcat ccgttcaccg
     1801 ttttttaaag tccgttaaaa gcatgatgcc atctccgaga gttaatctcg tcaaatgcta
     1861 aatcgtgggg gtcccctttg gggttccgat ttagtgattg acgacaccac cgattaaaaa
     1921 acttatgcgg ggtggatggt ttcacgaagt gaggccatcc acctgtaaga cagggttttg
     1981 tttttattcc ctgttttggt gatcgggtgt gtggaaaagg ttggggtaag ccgttcgggg
     2041 gtgcttgttt tggggggtta aaattgtggt tattttttgc gcaattctcg cgcgtgatcc
     2101 ttgtatttat acttaaggga taaatggcgg atatgaaata gtggtttagc ccagtaatga
     2161 cgaggctttg agtgggtttt gacaggtcaa agaaaatgga gcagaattga ggcgttttta
     2221 atcggcgttg gggagtgcgt caacactccc caacatttcg aatgtgtcac ctcagcggca
     2281 aactctggtg acatgtactg gctcgcaatg cacaggtacg tgatgaatat accacatcaa
     2341 atcacagcct gcccagatcg gagcaggctt aatgtcagaa gataaattcc tttcggacta
     2401 cagcccccgt gatgcagttt gggataccca gcgcacgctt accgattctg tcgggggtat
     2461 ctaccagact gctgctgaat tcgagcgcta tgcactccgt atggcctcct gtagcggtt
//
