LOCUS       NZ_CP012629             4072 bp    DNA     circular CON 11-JUN-2024
DEFINITION  Escherichia coli strain SF-468 plasmid pSF-468-4, complete sequence.
ACCESSION   NZ_CP012629
VERSION     NZ_CP012629.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN04026228
            Assembly: GCF_001280345.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4072)
  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 4072)
  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_001280345.1-RS_2024_06_11
            Annotation Date                   :: 06/11/2024 02:21:39
            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)                     :: 5,367
            CDSs (total)                      :: 5,248
            Genes (coding)                    :: 5,017
            CDSs (with protein)               :: 5,017
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 231
            CDSs (without protein)            :: 231
            Pseudo Genes (ambiguous residues) :: 0 of 231
            Pseudo Genes (frameshifted)       :: 98 of 231
            Pseudo Genes (incomplete)         :: 137 of 231
            Pseudo Genes (internal stop)      :: 46 of 231
            Pseudo Genes (multiple problems)  :: 46 of 231
            Pseudo Genes (short protein)      :: 1 of 231
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP012629.1.
            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..4072
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SF-468"
                     /isolation_source="patient blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSF-468-4"
                     /geo_loc_name="USA: San Francisco"
                     /lat_lon="37.755651 N 122.404572 W"
                     /collection_date="2010-04-05"
                     /collected_by="SFGH"
     gene            340..1032
                     /locus_tag="AN206_RS27240"
                     /old_locus_tag="AN206_27330"
     CDS             340..1032
                     /locus_tag="AN206_RS27240"
                     /old_locus_tag="AN206_27330"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /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_001281403.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCISRLKSGADAELQKT
                     MTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKNDEKREEFRWIQYRAQYAKG
                     EAKARITFSDAVMPYLTQLKGQFTRVVIKNISGLSSSYSIRIYEFLQQFRSTGERIIAL
                     NDFRSMLGIENKYKQFRDLNKILIKPCVDELNKKSDLAVTVETIKKGRTVVALHFRFKE
                     DKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(1288..3447)
                     /gene="mobQ"
                     /locus_tag="AN206_RS27245"
                     /old_locus_tag="AN206_27335"
     CDS             complement(1288..3447)
                     /gene="mobQ"
                     /locus_tag="AN206_RS27245"
                     /old_locus_tag="AN206_27335"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_001029353.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAECRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     gene            3626..3880
                     /gene="mobC"
                     /locus_tag="AN206_RS27250"
                     /old_locus_tag="AN206_27340"
     CDS             3626..3880
                     /gene="mobC"
                     /locus_tag="AN206_RS27250"
                     /old_locus_tag="AN206_27340"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091747.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     Typing          complement(3090..3448)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.056"
                     /coverage="100.0"
                     /evalue="3.94e-177"
     Typing          3449..3625
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          341..1032
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.965"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(1292..3534)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.332"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tcttgcaaca cattgttttt attggttttt tgttttcagc gccccaagtt atccacaggc
       61 tcgccgttaa gtttttagat cttgttttta agatcttgtt tttaatactt gttttagggt
      121 caaaattcat taataaaatc aatatgttat agaggtatat gtggaggaat ttaaggtaaa
      181 ggtggaggaa tttaaggtgt ttaggtggag gaatttaagg taaaggtgga ggaatttaag
      241 gtgttattca cagaaatgtg aggatataaa aaaaaatatt ccacatttct tatttgtggg
      301 gcacattaaa gcatcaccac atttgaacgg gatctttgta tgtcggactt gattgcctac
      361 aagtcgaatg ctttggttga ggccagctac aagttgaccc tacaggaaca acgttttctg
      421 ttgctgtgta tcagtcgatt gaaatctggt gctgatgctg aattgcaaaa gacaatgacc
      481 attaccgctg cggaatattt tgattcattc cctgacatgg ggcggaaaaa tgccgaggtt
      541 cagttacagg aagcgatcga tcgtttatgg gacaggtcga tcattctcaa gaatgacgag
      601 aagcgtgagg agttccgctg gatccagtat cgggcacagt acgctaaagg tgaggccaag
      661 gctcgaataa ccttttctga cgcggtaatg ccttatctga cgcaactgaa ggggcaattc
      721 acgcgcgttg ttataaaaaa catatcaggt ttatcaagta gttacagtat aagaatatac
      781 gagttcctcc agcaattccg cagtacggga gagagaatta ttgctcttaa tgactttcgt
      841 tcaatgttag ggattgaaaa taaatacaaa caattcagag acttaaataa aatactaata
      901 aaaccctgtg ttgacgaact gaacaaaaaa agcgacctgg ctgtaacggt tgagacgatc
      961 aaaaaggggc gcacggttgt agccctgcat tttcgcttca aggaagacaa acagatcaag
     1021 atgacgatct aaaatcgatt ttaaggcacc taaaacgctc cctgctgcgt tttttttgtg
     1081 ttagtagtgc gaaggtacta ttgaagtgaa aaattgcgtc aaaagcgctc taatgcagcg
     1141 aaaaaagaac ccccaatttt tgggggcgga aaaacaaaac tatgcttgca ttatgtgtgt
     1201 gcttcttgca ttcatccctg tcgatgaaca tagaagaaca tcgacgaaca taacacgatg
     1261 ttaaacaaaa caaaatattg ttcacattca ctgtgaccaa ccgcgatcat gtctcctctc
     1321 ggtggtgtgt gttcttgcat cttcctcgcg ccgccattca tcccaggtac gattgaaacc
     1381 cagagagcgg aacagatgat ccggctgttt ttctggtgtg ttgacggcag caaaaagcgg
     1441 tgcctcacgg gttttcagat gaaactccat aagttccggc gcaggtgata tgtggctgtc
     1501 tgcatcgtga tttacggcaa caccataccc tgcataccgt aaccccttat cggtcagtgc
     1561 actgatgacc agctggctgt tatcggctga gggaacggca aacgcgggat acagcgtacc
     1621 attaagccgg acaacaccgc ccagagagtc atccacgccc atgaccagca aaagctgaag
     1681 ctggcgggtt tcccggtcga cagaactcat taccggcatc agcgtcggta gcagacgtcc
     1741 ctgcgtaaaa tccaccttcc ttgctgccag tgatggcatg gctggctggc ggtcttctcc
     1801 aagacagaaa gactccggcc atgtcttcgg ctggcggaga ttgcgggtat attgcggcca
     1861 tgtctggcaa acctgcgtca gaagttgctc aaaggtcgca gaggaataaa cacgttgcag
     1921 tggtggatgt tgaccgattt cgcttcggtc acagatataa ccactcctgt cacgcattaa
     1981 atcaacacgc tcaaagattc tggtgcggta tttctccagc tcgttccccc agagcgtgta
     2041 ttctccgttc cggttgtgaa gcagaaggta acaggtcatt tccccgttac caggcatggg
     2101 ggcctcgcca taccccgtaa cgactgcgct cagtacccct gaatccataa cggcattgtc
     2161 atttttcctg agctgttccg ctcgtcgctc cgcgcgacta cgttctgtat cctcctgctc
     2221 cttccggcgc aattcctctt cacgtttaag caactggact ctgagagctg caaggccgga
     2281 tgccccccac tgctgccact gtttttcaaa tgccgtctga ctcgcgggaa tgtcctgttt
     2341 ctccaccttc cggtaatgct gtcgcaattt ttccatttgc tggctcagcg actggatttt
     2401 tccctgttcg ctacggtatt ccggtgccgc ccattgcatc aggggaatac gggaaaaacc
     2461 ggacgaaaac ggcgatgatt ttttcaggct ggcagcatgg ctcatcgctt cctttcgttc
     2521 ggtgttcagc tcttcccagc gtctgcgcgt cgcctgcata tctgccatca tcgacatggc
     2581 attactggtg agtttccatg ccgcattact gtccttcggc aacgcttcga tgatgtcacg
     2641 tagtgtgtac gaagttgcgt tgtcaggaag cacgatattc agaaggtcag ccacacggcg
     2701 ggcaggctct gtcagcccgc tgttcctgag ttcagtgcgg gaaatctgta tttccaggtt
     2761 aagcctgtta atcagacgat tctgttcgcc gcgttctgtt tcgataccgc gtgtttccat
     2821 cgcacaggca gactttccga ggtgaatacc aggcgttttc tcaagcccct gtcgctcgta
     2881 tgaacgatgg tctatctctt cctgataacc ggcgttcgcc agtgctctgt ttgcatggtc
     2941 agcccatgat gcacgccacg tctcggcatg tgtccggtcg ttccagtccc tgacctttcc
     3001 gccgaaccca gcaggtccga cagccctcgt ggtcagcatg atgtgcgcat ggggatttgt
     3061 tttatccatg tgatggaacg ccacatcagc aatcatgccc tgactgacaa agttttctct
     3121 gacaaaggcg agaacggttt cccgtgcggc atcctgcggc agttcacggg ggatagcgag
     3181 ttcaatttcc cgcgcaagtt gtgagttctt ccggcattcg gccttctcaa cggcattcca
     3241 gagttcggca cggttcgtac accaggcagg ggctgtcgcg ggggtcagaa tcacagcttc
     3301 agccacaccg cttttgcggg tgtagtcgtg agtcagtccg gtacgctcat caagcatcag
     3361 tgaaccggaa cgataggcag cggaagctac ggcgctgtag ccgctgcttc tggagataat
     3421 tttcatgctg agatgataaa tcgccatttc tgccgtaatg cctttttgta gttttctttc
     3481 agccccgcag ggcgcacaca atcgaaacgg agtggagatt gtataagtgc gcactttgtg
     3541 atttgtcgcg cattatgcca gctcagtttt taaactacca gtgacgcgct aaaatgcgat
     3601 ttttcatcgc gcacggagtt acatcatgag cagaacgctc gaacagaaga ttgctgatgc
     3661 tgaggcgaga ttacagcgcc tgaaggcgaa gagccggagc ctggacacag cgcagaaggt
     3721 tgttgtgggt gcagcattgc tggcaaaggt cagaaagccg gaggaggtgc agttgcgtgc
     3781 ctggttactc cagttcctga aggcagaggt gacacgacag gctgatgtga cgcgcatact
     3841 gccgctgatt aacgagctgg aggcgctgcc aggacagtga ttgtatcgtc cgctcgccgc
     3901 agccccagcg accgagcgtt agcgagcgag tgggcgagga agcggaagtg aatccgtcgc
     3961 caggttgagc acatacgcac ggtttttcgg taggtgatat gcgctgaacc cgcatgaata
     4021 ctggatttcc acagggttgg aaggggagta ttcggaactt gcaattctgc tt
//
