LOCUS       NZ_CP012637             5167 bp    DNA     circular CON 11-JUN-2024
DEFINITION  Escherichia coli strain SF-088 plasmid pSF-088-2, complete sequence.
ACCESSION   NZ_CP012637
VERSION     NZ_CP012637.1
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 5167)
  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 5167)
  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
            CP012637.1.
            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..5167
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SF-088"
                     /isolation_source="patient blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSF-088-2"
                     /geo_loc_name="USA: San Francisco"
                     /lat_lon="37.755651 N 122.404572 W"
                     /collection_date="2007-09-06"
                     /collected_by="SFGH"
     gene            438..1352
                     /locus_tag="AN203_RS26260"
                     /old_locus_tag="AN203_26310"
     CDS             438..1352
                     /locus_tag="AN203_RS26260"
                     /old_locus_tag="AN203_26310"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001738986.1"
                     /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_001271348.1"
                     /translation="MSAALQYFDENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWLVMEWREEAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLEAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGSKSKRSTVATSARTL
                     KPWEALGISRAWYYQLKKRGLVE"
                     /name="replication initiation protein"
     gene            complement(1556..1954)
                     /locus_tag="AN203_RS26265"
                     /old_locus_tag="AN203_26315"
     CDS             complement(1556..1954)
                     /locus_tag="AN203_RS26265"
                     /old_locus_tag="AN203_26315"
                     /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_001222914.1"
                     /translation="MRISNIEWLKKRIGFIRKLGEQTARQRQIIDLIDNEAGLTEQERK
                     LLHVLATAEKNDLQAQESERKQAVQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELCYKKDRILQALKELKYDLETSPNPDA"
                     /name="hypothetical protein"
     gene            2131..3057
                     /locus_tag="AN203_RS26270"
                     /old_locus_tag="AN203_26320"
     CDS             2131..3057
                     /locus_tag="AN203_RS26270"
                     /old_locus_tag="AN203_26320"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221102.1"
                     /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_001331297.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTPEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIDGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     LTQQKEQLRELRKRWEVKHNEHMRKHGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIREWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQNRTAPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            3060..3593
                     /locus_tag="AN203_RS26275"
                     /old_locus_tag="AN203_26325"
     CDS             3060..3593
                     /locus_tag="AN203_RS26275"
                     /old_locus_tag="AN203_26325"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221103.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000168770.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQKLDVAGLIGERISQDFQRLEESVANMKANADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFCVLGWGMKTILDRNYNATAAVYQKVVTLED
                     KLVEKPVTGKSRKN"
                     /name="hypothetical protein"
     gene            complement(3659..3868)
                     /locus_tag="AN203_RS26280"
                     /old_locus_tag="AN203_26330"
     CDS             complement(3659..3868)
                     /locus_tag="AN203_RS26280"
                     /old_locus_tag="AN203_26330"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001618649.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001096196.1"
                     /translation="MAKLGENTPHIIDATVDFMASSQAFREYLKKLPPDNTIPPALTDE
                     HVPLYIRRLEYYRLLYRPKQTESY"
                     /name="hypothetical protein"
     Typing          439..1213
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.778"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          2132..3054
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.052"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gttttttttt gtcctggcga gatgtgaagt ttggaaacag gaaaccccgt cagagcgcca
       61 cgcaccaggg gagaaaactt gtcgttttga gccgttcggt gttcagaacg cacgaaaccg
      121 atcgcacatc gctttcgtgc atagttatgc aacgccctga aaacgattct gacgcgtttt
      181 tctggtttgg cctggtgttt tcttgtcttt ttgcgttttt tgcgccagaa agcgactgag
      241 ggcgttttaa ggggggcgta caacgggagt tatggtaaat ggatcgggtt ttcgggaagg
      301 ttcgacagga tttgccgttg ggtgtagtgt aagcgactga aaaacaaacg cccctgaaat
      361 catgtccaga tccggcaaga ttcaacatga aatacagagg gcgtgtaggt cgcataaccc
      421 ggagagaatc gtaacacatg agcgccgcgc ttcaatactt cgacgaaaat ttaccccatc
      481 gtccctatca cacggatgat ctcgcttttg gtcttcgcat ctccggcaaa gggcgtgcgc
      541 ttcttgcgcg gtacatacag cagaaccagc ctcatgcgca gttctggctg gtttttgacg
      601 ttgaccgcga gggggctgcg attgactgga gcgaccggaa cgctcccgcg ccgaacatca
      661 ccgttaaaaa tcctgtgaac ggacacgctc acctgctcta cgcactcaac atcgccgtga
      721 gaaccgcgcc tgatgcctcg gttaaggcgc tgaaatatgc cgcagcggtt gaacgttcgc
      781 tgtgtgagaa actttgtgcg gatgtgaact acagcggcct gatttgcaaa aatccgttcc
      841 acctggaatg gctggtgatg gagtggcgcg aggaagccta taccctcgat gaactggctg
      901 attatctcga tttgagcgcc tcagagcgtc gtagcatcga taaacattac gggatggggc
      961 gaaactgcca cctgttcgaa atgacgcgca aatgggctta cagggcgatt cgtcagggct
     1021 ggccagcgtt ctcacagtgg cttgaagcgg tgatccagcg tgtcgaaatg tacaatgcat
     1081 cgcttcccgt tccgctttca ctggctgaat gtcgggctat tggcaagagc attgcgaaat
     1141 acacgcacag gaacttcacg ccggaaactt tcgcacagta tgtggctgat acgcacacgc
     1201 cagaaattca ggctgcacgc ggtcgcaagg gcggttctaa gtctaagcgc agcacagtag
     1261 ctacatctgc acgcacgctg aaaccgtggg aggcattagg gatcagtcgc gcctggtatt
     1321 accaactgaa aaaacgaggt ctcgtagagt agaccaaata agcctatatc agataacagc
     1381 gcctttctgg cgtctttttg agcagcaggt tttttgccgt ttttccccgt tcagccctgc
     1441 aatggcgcgg ctttccgcgt gattgtggtg gtagtgctcg ccgcagtctc atgaccgagc
     1501 gtagcgagcg aatgagcgag gaagcaccag ggaatcggaa cacggatgga ggcacttacg
     1561 cgtctgggtt tggggatgtc tccagatcgt acttaagttc cttaagtgct tgtaatatcc
     1621 tgtctttttt atagcatagc tcgcctgttt ttgtgtctac cagtcctgct tcgatcagta
     1681 gcccagccgc gagaaagagc cggtgattgc gttcccgtcg ttgttttttt ccctcgattc
     1741 gtttttggac cgcctgtttt cgttcgctct cctgtgcctg taagtcgttt ttttccgctg
     1801 ttgccagtac gtggagaagt ttgcgttcct gttctgtgag tccggcttcg ttgtcgatca
     1861 ggtcaataat ctgtctctgt cgtgcggtct gttctccgag cttcctgatg aatccgatcc
     1921 gtttcttcag ccattcgatg ttgctgatgc gcatgttcgt gatgctccct ggtgtttttt
     1981 tgcggtgtgt tgtggtcgtg cagtatatcg cttgcggtcg gcgggtgcag ggggtatctt
     2041 ccgtgctaat tcgtaaaatt agaaggaagc gcacttatat gtttctctcc ttcgtcgaga
     2101 aacagtgcgc tcctgcagag ggctgaaacc gtggcaacct atcacctcag cgttaaattt
     2161 ggtggcaagg ggcaggctgc aaaccacgcc gattacatcg agcgcaaaga gaaataccgc
     2221 gaccgtcagg atttggaata ttccgcacac ggaaacatgc cggaatgggc cagggataat
     2281 ccttcccatt tctggcaggc ggctgaccag tttgaacgtg cgaacggttc gacctatagg
     2341 gaacttgaaa ttgcattacc ccgtgaactg acaccggaac agcgccttga actggtgcag
     2401 gattttgtac gtcaggaagc tggcgaacgg cacgcctgga gttttgccat tcacaatccg
     2461 aaagcgagca ttgacggcgg cgaacagcct catgcgcata tcatgatgag tcagcgtgtg
     2521 aatgatggca ttgaacgtac accggaacag tatttccggc gctataacgc caggtatccc
     2581 gagcggggag gtgcgaaaaa ggattccgga agcctgactc tcactcagca aaaagagcag
     2641 ttgcgggaat tgcgaaaacg ctgggaggtg aagcacaacg aacatatgag aaagcatggc
     2701 tttgaaaggg gcttcattga ctgccggacg ctgaaagaac agggcattga acgacgtccc
     2761 gaagtgcatc tgggttttga agctgccgga cggcttgatg atgcccagcg tcatgacatc
     2821 atgcaaaaac ggtctgaacc ggactattcc cgccatcttg aacaggcgcg aacggtcggg
     2881 catgacatca gggaatggct ggacactccg gttaagcaac atgaactggt cagaaggctg
     2941 caacatgatg ttgcgcggga gcatggcttt gacatgagag acagagtgag cagacagaac
     3001 cgaactgcac ctgaacgggt taaatcaccg tcacgtggat tttctatggg attctgaaca
     3061 tggccagcac agaagaaaaa ttacttacgc tcctgttatc ggtggagcat ctgcaacata
     3121 ccgcaatgga gcaacagaaa gctgttgctg attctctggc tgtggcaagg gaaactcttc
     3181 gcggatatcg ggatatttct gacggtgtgg caaaacaggt cagggatgaa gtcagaaatg
     3241 aggtgcagaa gctggacgtg gcaggactga taggtgagcg catcagccag gattttcagc
     3301 ggctggaaga gtcagtcgca aacatgaagg caaacgcgga tgccctgaac agggatattg
     3361 cgacaattca cagcaatatc gtgcaggaat acaacaccct taaagggtat agctggaaat
     3421 ggctgggtgg ggtgtcagtg gcttttctgg ttatgttctg tgtgctcgga tggggaatga
     3481 aaacaatact cgacaggaac tacaacgcca cagcggcggt gtatcagaaa gttgtgacac
     3541 tggaagataa actggtggag aaacctgtca cggggaagag ccggaaaaac tgacgcgctt
     3601 cgcttgtcca acgcctcacg acccgcgaaa gaatttcgcg aaccgttcac cgtttttttc
     3661 aatatgattc tgtctgcttt ggtcgataaa gcagacgata gtattccagc cttcgtatat
     3721 ataacggtac gtgctcatca gtaagagctg gcggtattgt gttatcaggg ggaagttttt
     3781 tcagatactc acgaaatgcc tggcttgatg ccataaaatc tacagtagca tcgataatat
     3841 gtggggtgtt ttcacctaat tttgccatga tgataatcct tatattatca cggtttgtga
     3901 atgatagggt gtcactatta tttatgcgtt agtgaaccag aaaaaatccc ccgttggcat
     3961 agggggatat gtaaggagaa ataacttcgc aggtgttctt gtttgtataa cgtgaaaaga
     4021 ctgcacgcaa cttaataagt ctgccgtact tactttcagt tttcaacata aggtttataa
     4081 caatgtatgg aatggaagtg agctttaagg tttcagctct aaaaaataaa atatttatta
     4141 gttggctggt tgttgttctt gttctgtatg tatataaaca ctatcgacat attatgaccg
     4201 ggaacattcc ttaccccctc tgcgctcgca gaggtttttt ttgtcattaa ttaataatga
     4261 actgaaatgc agttccgata cctccatttg cacattatcc ctgacatatg gtaccggaac
     4321 cgcattaatt ttatgttata agagtttatt tttaatgtcc agatggttta atagtattta
     4381 tatgtaatta gctgtatgga tagtactggt tttattgtat aacttgtcgt ttttttttat
     4441 tgtttttgtg tggtgtgcta atctttaagt tataaaaaaa ccccttggaa tacaggggca
     4501 aaagtaagga aaacaaatgg atgctcagtt tgtgtgacac tttaaactaa tggaactata
     4561 gagtggaggt tgttacagtc gcttttataa aacagcaacc agtttttttc aatagtctga
     4621 tgatggttgt gacagttttg tgatattgtt caaaatgttt cttgttgaat gtttgttttt
     4681 tggtctattg gtgtctggtt ttattttttc tgctattaca tatcaagaaa tgtgattggt
     4741 gtagcaagag tggaatgcga tgtggataaa ctaattggtt gtcgaatcta atttacttag
     4801 aaaactacac ttgtttttgt gtatgaattt agtgaatttg tctgtctatg tgttttcgtg
     4861 catttataaa tccttcgtca ggatcttaaa tttagtgttg aatatgtagg gcctgtacgg
     4921 taattattat ttagcgtagc tacttcatcg ttgttcgaac acaaccaaca acctgtaatt
     4981 gttgtttctc ttggttcccc acttttgtgg ggttttttat ctcttccgtg catcgtaaag
     5041 cgcggactcc ttctggaaag gttgttttag ggcatcactg aggcattttt tgcgtttgtg
     5101 aatattgagc atccgataac taaaatattt cccatagact ctgattcttg ccaccgaccc
     5161 caggtcg
//
