LOCUS       NC_010486               4074 bp    DNA     circular CON 01-JUN-2024
DEFINITION  Escherichia coli SMS-3-5 plasmid pSMS35_4, complete sequence.
ACCESSION   NC_010486
VERSION     NC_010486.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN02604066
            Assembly: GCF_000019645.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli SMS-3-5
  ORGANISM  Escherichia coli SMS-3-5
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4074)
  AUTHORS   Fricke,W.F., Wright,M.S., Lindell,A.H., Harkins,D.M.,
            Baker-Austin,C., Ravel,J. and Stepanauskas,R.
  TITLE     Insights into the environmental resistance gene pool from the genome
            sequence of the multidrug-resistant environmental isolate
            Escherichia coli SMS-3-5
  JOURNAL   J Bacteriol 190 (20), 6779-6794 (2008)
   PUBMED   18708504
REFERENCE   2  (bases 1 to 4074)
  AUTHORS   Fricke,W.F., Wright,M.S., Lindell,A.H., Harkins,D.M.,
            Baker-Austin,C., Ravel,J. and Stepanauskas,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (14-MAR-2008) J. Craig Venter Institute, 9712 Medical
            Center Dr, Rockville, MD 20850, USA
COMMENT     ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_000019645.1-RS_2024_06_01
            Annotation Date                   :: 06/01/2024 01:33:08
            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)                     :: 5,037
            CDSs (total)                      :: 4,920
            Genes (coding)                    :: 4,705
            CDSs (with protein)               :: 4,705
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 215
            CDSs (without protein)            :: 215
            Pseudo Genes (ambiguous residues) :: 0 of 215
            Pseudo Genes (frameshifted)       :: 93 of 215
            Pseudo Genes (incomplete)         :: 155 of 215
            Pseudo Genes (internal stop)      :: 48 of 215
            Pseudo Genes (multiple problems)  :: 64 of 215
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP000973.1.
            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..4074
                     /organism="Escherichia coli SMS-3-5"
                     /mol_type="genomic DNA"
                     /strain="SMS-3-5"
                     /db_xref="taxon:439855"
                     /plasmid="pSMS35_4"
     gene            165..866
                     /locus_tag="ECSMS35_RS25790"
                     /old_locus_tag="EcSMS35_C0001"
     CDS             165..866
                     /locus_tag="ECSMS35_RS25790"
                     /old_locus_tag="EcSMS35_C0001"
                     /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_001281397.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCIGRLKSGADAESPKL
                     QKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRAQY
                     AKGEARAQITFSDAVMPYLTQLQGQFTRVVIKNISRLSRSYSIRIYELLQQFRSTGERI
                     IALDDFRSMLDIEHKYQTYKSLNQQLLRPCIDELNKKSDLAVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(1114..3273)
                     /gene="mobQ"
                     /locus_tag="ECSMS35_RS25795"
                     /old_locus_tag="EcSMS35_C0002"
     CDS             complement(1114..3273)
                     /gene="mobQ"
                     /locus_tag="ECSMS35_RS25795"
                     /old_locus_tag="EcSMS35_C0002"
                     /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_001029346.1"
                     /translation="MAIYHLSMKIISRNSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNNRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRMADLLNIGLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFETQWQQWGASGLAALRAQL
                     LKREEELRRKEQEDTERRRAERRAEQLRQNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     SYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQHTRNLRQPKTWPEFFCLGEDRQPAMPSLAARKVDFTQGRLPPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNSTLYPAFAVPSADNRHLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHATERRRDRGWSQ"
                     /name="mobQ"
     gene            3452..3706
                     /gene="mobC"
                     /locus_tag="ECSMS35_RS25800"
                     /old_locus_tag="EcSMS35_C0004"
     CDS             3452..3706
                     /gene="mobC"
                     /locus_tag="ECSMS35_RS25800"
                     /old_locus_tag="EcSMS35_C0004"
                     /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_000091744.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     Typing          complement(2916..3274)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3275..3451
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          166..866
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(1118..3360)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.861"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 taaaggtaat atgatttaag gtgtttaggt aatatgattt aaggtaaagg caatatgatt
       61 taaggtaata ttcacagaaa aagggatatt aaaataaaaa ggcattgcct ttcgttgagg
      121 gtatgtttat cttttattca ttaccttttg gggagggatg ctctatgtcg gatctaattg
      181 cctataaatc caatgcgctg gttgaagcca gttataaatt gaccctacag gaacagcgat
      241 ttttgttact ttgcatcggt cgattgaagt ctggggctga tgcagaatct ccaaaattgc
      301 aaaagacaat gaccattaca gctgcggaat atttcgattc attccctgac atggggcgga
      361 aaaatgccga ggttcagtta caggaagcaa ttgatcgttt gtgggacagg tcaatcattc
      421 tcaaggatga cgagaaacgt gaggagttcc gctggatcca gtatcgggca cagtacgcta
      481 aaggcgaggc cagagcacaa ataacatttt ctgacgcagt aatgccttat ttgacacaac
      541 tacaagggca atttactaga gttgtaatca agaatatatc tagattatca agaagttaca
      601 gtataaggat atacgaactc ctccagcagt tccgcagtac tggcgaacgt attatcgctc
      661 tcgatgattt tcgctcaatg cttgatatag agcataaata tcaaacatat aaatcactta
      721 accagcaatt attaagaccc tgcattgacg aactgaacaa aaaaagcgac ctggctgtaa
      781 cggttgagac gatcaaaaag gggcgcacgg ttgtagccct gcattttcgc ttcaaggaag
      841 acaaacaaat caagatgacg atctaaaatc gattttaagg catctaaaac gcgctctggt
      901 gcgttttttt tgcgtaaggt atgcgatggt gctacgaagc acaaaaacat cgtcagaatc
      961 gctctcgcga gctaaaaaaa tcccccatat acggggggga agaaactatg cggagattat
     1021 ctagtttgtt gtgtgtgctt cttgcattca tccctgtcga tgaacattga agaacataac
     1081 atgatgtaaa acaaaacaaa atattgttca cattcactgt gaccaaccgc gatcgcgcct
     1141 cctctcggtg gcgtgtgttc gtgcatcttc ctcgcgccgc cattcatccc aggtacgatt
     1201 aaaacccagc gagcggaaca gatgatccgg ctgtttttct ggtgtgttga cggcagcaaa
     1261 aagcggtgcc tcacgggttt tcagatgaaa ctccataagt tccggtgcag gtgatatgtg
     1321 gctgtctgca tcgtgattga cggcaacacc ataccctgca taccgtaacc ccttatcggt
     1381 cagcgcactg atgaccagat gcctgttatc ggctgaggga acggcaaacg cgggatacag
     1441 cgtactatta agccggacaa caccgcccag agagtcatcc acgcccatga ccagcaaaag
     1501 ctgaagctgg cgggtttccc ggtcgacaga actcattacc ggcatcagcg tcggtggcag
     1561 acgtccctgc gtaaaatcca ccttccttgc tgccagtgat ggcatggctg gctggcggtc
     1621 ttctccaaga cagaaaaact ccggccatgt cttcggctgg cggagattgc gggtatgttg
     1681 tggccatgtc tggcaaacct gcgtcagcag ttgctcaaag gtcgcagagg aataaacacg
     1741 ttgcagtggt ggatgttgac cgatttcgct tcggtcacag atataaccac tcctgtcacg
     1801 cattaaatca acacgctcaa agattctggt tcggtatttc tccagttcgt tcccccagag
     1861 cgtatattct ccgttccggt tgtgaagcag aaggtaactg gtcatttccc cgttaccagg
     1921 catgggggcc tcgccatacc ccgttacgac cgcactcagt acccctgaat ccatgacggc
     1981 attgtcattt tgcctgagct gctcagcccg tcgctccgcg cgacgacgtt ctgtgtcctc
     2041 ctgctccttc cggcgcaatt cctcttcacg tttaagcaac tgggctctga gagctgcaag
     2101 gccggatgcg ccccactgct gccactgtgt ttcaaatgcc gtctgactcg cgggaatgtc
     2161 ctgtttctcc accttccggt aatgctgtcg caatttttcc atttgctggc tcagagactg
     2221 gatttttccc tgctcactgc ggtattccgg tgccgcccat tgcatcaggg gaatacggga
     2281 aaaaccggac gaaaacggcg atgatttttt caggctggct gcatggctca tagcttcctt
     2341 ccgttcggtg ttcagctctt cccagcgtct gcgcgtcgcc tgcatatctg ccatcatcga
     2401 catggcatta ctggtgagtt tccatgccgc gttactgtcc ttcggcaacg cttcgatgat
     2461 gtcacgtagt gtgtacgaag ttgcgttgtc aggaagcccg atattcagaa ggtcagccat
     2521 acggcgggca ggctctgtca gcccgctgtt tctgagttcg gtacgggaaa tctgtatttc
     2581 caggttaagt ctgttaatca gacgattctg ttcgccgcgt tctgtttcga taccgcgtgt
     2641 ttccatcgca caggcagact ttccgaggtg aataccaggc gttttctcaa gcccctgtcg
     2701 ctcgtatgaa cgatggtcta tctcttcctg ataaccggcg ttcgccagtg ccctgttcgc
     2761 atggtcagcc catgatgcac gccacgtctc ggcatgtgtc cggttgttcc agtccctgac
     2821 ctttccaccg aatccagcag gtccgacagc tctcgtggtc agcatgatgt gcgcatgggg
     2881 atttgtttta tccatgtgat ggaacgccac atcagcaatc atgccctgac tgacaaagtt
     2941 ttctctgaca aaggcgagaa cggtttcccg tgcggcatcc tgcggtagtt cgcgggggat
     3001 ggcgagttca atttcccgcg caagttgtga gttcttccgg cgttcggcct tctcaacggc
     3061 attccagagt tcggcacggt tcgtacacca ggcaggggct gtcgcgggag tcagaatcac
     3121 agcttcagcc acaccgcttt tgcgggtgta gtcgtgagtc agtccggtac gctcatcaag
     3181 catcagtgaa ccggaacgat aggcagcaga agcaacggcg ctgtagccgc tgtttctgga
     3241 gatgattttc atgctgagat gataaatcgc catttctgcc gtaatgcctt tttgtggttt
     3301 tctttcagcc ccgcagggcg cacacaatcg aaacggagtg gagattgtat aagtgcgcac
     3361 ttcgtgattt tccgtgcatt atgccagctc agtttttaaa ctaccagtga cgcgctaaaa
     3421 tgcgattttt catcgcgcac ggagttacat catgagcaga acactcgaac agaagattgc
     3481 tgatgctgag gccagattac agcgcctgaa ggcgaagagc aggagtctgg acacagcgca
     3541 gaaggtcatt gtgggtgcag cattgctggc aaaggtcaga aagccggagg aggtgcagtt
     3601 gcgtgcctgg ttactccagt tcctgaaggc agaggtgaca cgacaggctg atgtgacgcg
     3661 catactgccg ctgattaacg agctggaagc gctgccagaa cagtgattgt atcgtccgct
     3721 cgccgcagtc ccagcgaccg agcgttagcg agcgagtggg cgaggaagcg gaagtgaatc
     3781 cgtcgcctga ttgagcacat acgcacggtt tttcgggagg tgatatgcgc tgaacccgca
     3841 tgaatactgg atttccacag ggttggaggg ggtgtattcg gaacttgcaa ttctgctttt
     3901 ttgcaacgca ttgtttttat tggttttttg ttttcagcac tccaagttat ccacaggctc
     3961 gtcgttaagt ttttagatct tgtttttaag atcttgtttt taatacttgt tttagtgcca
     4021 aaattcccta tagaaaacaa aatgttacaa cgctataggt aatatgattt aagg
//
