LOCUS       NZ_CP029445             6393 bp    DNA     circular CON 28-JAN-2024
DEFINITION  Serratia marcescens strain CAV1761 plasmid pCAV1761-6393, complete
            sequence.
ACCESSION   NZ_CP029445
VERSION     NZ_CP029445.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN09205456
            Assembly: GCF_003146705.1
KEYWORDS    RefSeq.
SOURCE      Serratia marcescens
  ORGANISM  Serratia marcescens
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Yersiniaceae; Serratia.
REFERENCE   1  (bases 1 to 6393)
  AUTHORS   Mathers,A.J., Vegesana,K., Stoesser,N., Crook,D., Vaughan,A.,
            Barry,K., Parikh,H., Sebra,R., Kotay,S., Walker,A.S. and
            Sheppard,A.E.
  TITLE     Klebsiella quasipneumonaiae provides a window into carbapenemase
            gene transfer, plasmid rearrangements and nosocomial acquisition
            from the hospital environment
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6393)
  AUTHORS   Mathers,A.J., Vegesana,K., Stoesser,N., Crook,D., Vaughan,A.,
            Barry,K., Parikh,H., Sebra,R., Kotay,S., Walker,A.S. and
            Sheppard,A.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (16-MAY-2018) Nuffield Department of Medicine, University
            of Oxford, John Radcliffe Hospital, Oxford OX39DU, United Kingdom
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. MAY-2015
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 36x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/28/2024 10:29:17
            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)                     :: 5,741
            CDSs (total)                      :: 5,616
            Genes (coding)                    :: 5,494
            CDSs (with protein)               :: 5,494
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 123
            CDSs (without protein)            :: 122
            Pseudo Genes (ambiguous residues) :: 0 of 123
            Pseudo Genes (frameshifted)       :: 44 of 123
            Pseudo Genes (incomplete)         :: 83 of 123
            Pseudo Genes (internal stop)      :: 16 of 123
            Pseudo Genes (multiple problems)  :: 18 of 123
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP029445.1.
            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..6393
                     /organism="Serratia marcescens"
                     /mol_type="genomic DNA"
                     /strain="CAV1761"
                     /isolation_source="Peri-rectal"
                     /host="Homo sapiens"
                     /db_xref="taxon:615"
                     /plasmid="pCAV1761-6393"
                     /geo_loc_name="USA:Virginia"
                     /lat_lon="38.14 N 78.45 W"
                     /collection_date="2014-03-01"
                     /collected_by="Clinical Microbiology University of Virginia
                     Health System"
     gene            172..597
                     /locus_tag="DKC05_RS00030"
                     /old_locus_tag="DKC05_00035"
     CDS             172..597
                     /locus_tag="DKC05_RS00030"
                     /old_locus_tag="DKC05_00035"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001676030.1"
                     /GO_function="GO:0005515 - protein binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="PH domain-containing protein"
                     /protein_id="WP_015328245.1"
                     /translation="MGSYVDQSLTRNESVISRAQTSWIPTIIPVIIGILLLPFYGLGLL
                     IIIPVLLRVWSTELALTNQRVIAKVGLIRRNTVELRIDKVESLGIHQGILGRIFNYGSI
                     VIKGTGGTNTPIPNIKAPMQFRSIVNNHIEEMNSKQQ"
                     /name="PH domain-containing protein"
     gene            862..1050
                     /locus_tag="DKC05_RS00035"
                     /old_locus_tag="DKC05_00040"
     CDS             862..1050
                     /locus_tag="DKC05_RS00035"
                     /old_locus_tag="DKC05_00040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041625.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_047727531.1"
                     /translation="MNRQESAALNMAKFIRAQTLLLLEKIDQLDLDDEATDCEKLHEQA
                     EKLYQKLQARLDSDITQ"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(1033..1215)
                     /locus_tag="DKC05_RS00040"
     CDS             complement(1033..1215)
                     /locus_tag="DKC05_RS00040"
                     /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_143350598.1"
                     /translation="MSSNAEWYIGHAVVELLVQERVVSMFSVIDILERRLQSGDSSKDE
                     FMEILEAIEKLLGYV"
                     /name="hypothetical protein"
     gene            complement(1563..2168)
                     /locus_tag="DKC05_RS00045"
                     /old_locus_tag="DKC05_00045"
     CDS             complement(1563..2168)
                     /locus_tag="DKC05_RS00045"
                     /old_locus_tag="DKC05_00045"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001549957.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0000150 - DNA strand exchange activity [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="recombinase family protein"
                     /protein_id="WP_000509966.1"
                     /translation="MGHRAAIYCRVSTADQSCERQEFDLRAFAGRAGYDVVGIFKETGS
                     GTKLDRAERKKVLALAQSRQIDAILVTELSRWGRSTLDLLNTLRELENWKVSVIAMNGM
                     AFDLSSPYGRMLATFLSGIAEFERDLISERVKSGLAVAKARGKRLGRQAGVRPKSDRLL
                     PKVVAMRAEGRSYRWIARELGISKNTVADIVQRHRANA"
                     /name="recombinase family protein"
     gene            2263..5160
                     /locus_tag="DKC05_RS00050"
                     /old_locus_tag="DKC05_00050"
     CDS             2263..5160
                     /locus_tag="DKC05_RS00050"
                     /old_locus_tag="DKC05_00050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020326821.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Tn3-like element Tn5403 family transposase"
                     /protein_id="WP_004206881.1"
                     /translation="MSRRHIFTERQRAALFDLPTDELSLLKFYTLGDDDLENIRQRRRP
                     ENRIGFALQLCALRYPGRALAPGEMIPREILSFVGAQLGVPADALLTYATRRQTRQQHM
                     DTLREIYGYKTFTGRGARDLREWTFGQAEDARSNEDLAHRFIVRCRETSTILPAVSTIE
                     RLCADALVAAERRIETRIVENLTADVRDHLDKLLSEMLAGNISRFIWLRNFEVGNNSAA
                     ANRLLDRLEFLRTLNINHSALASIPAHRIARLRRQGERYFTDGLRDITSDRRWAILAVC
                     VVEWEAAIADAIVETHDRIVGKTWREAKRQHDETISGSKATLADTIRTFTALGASLLEA
                     RSDGTPLEMAVASSVAWDRLAQLVATGTQLSNTLADEPLAYVGQGYHRFRRYAPRMLRC
                     LKLEAAPVAGPLVAAALSIGEMKGVASPERRFLRPSSKWNRHLRAQEKGDTRLWEVAVL
                     FHLRDAFRSGDVWLAHSRRYGDLKQVLVPMIAAQENAKLAVPSNPQDWLADRKARLTIA
                     LKRLARAARNGTIPHGSIEDGTLRIDRLTADVPDGAEALILDLYRRMPSVRITDMLLEV
                     DAALGFTDAFTHLRTGAPCRDRIGLLNVLLAEGLNLGLRKMAEATNTHDYWQLSRLARW
                     HVESEAMNQALAIVVAAQGKLPMSRVWGMGTSASSDGQFFPTARHGEAMNMVNAKYGSV
                     PGLKAYTHVSDQFAPFACQSIPATVSEAPYILDGLLMNEVGRHVREQYADTAGFTDHLF
                     GASSLLGYNLVLRIRDLPSKRLYVFNPDTTPRELRKLVGGKAREDLIVANWPDIFRCAA
                     TMTAGKIRPSQLLRKLASYPRQNNLAVALREVGRIERTLFIIEWILDTDMQRRAQIGLN
                     KGEAHHALKNALRIGRQGEIRDRTTEGQHYRIAGLNLLTAVIIYWNTVHLGHAVTERRN
                     EGLDVPPEFLPHISPLGWAHILLTGEYLWPKEPKA"
                     /name="Tn3-like element Tn5403 family transposase"
     Typing          complement(5472..5650)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="88.525"
                     /coverage="83.0"
                     /evalue="1.6099999999999998e-54"
     Typing          5630..6114
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.206"
                     /coverage="93.0"
                     /evalue="3.54e-169"
ORIGIN
        1 ccaccatcac agaatcaagc cagttgcggc acgaaaggaa agaaccgaac tgtgcgacgg
       61 tcgctacgct ctccgtaaat tttgtatacc taccacggag acataaagtt tctattgctg
      121 attcgcctta aaaagggaaa aatcctattt tttctaaatg gatataacct tatgggaagc
      181 tacgtagacc aatcattgac gagaaatgaa tccgtaatat ctcgcgctca aacctcctgg
      241 attccaacaa tcatcccagt aattatcgga atcttgttgc tgccttttta cggcttaggg
      301 ttacttataa taatccctgt gctccttaga gtttggtcaa cggagcttgc attaactaac
      361 caaagagtca tcgcaaaagt gggtttgatc cgacgcaata cggtggaact ccgtattgat
      421 aaagttgaaa gccttggcat acatcaaggg atactgggac gaatctttaa ctatgggtct
      481 atcgtgatta aaggcactgg cggaaccaac actccaattc caaacatcaa ggcgccaatg
      541 caattcagat cgattgtgaa caatcatatc gaggaaatga attctaagca gcagtagctt
      601 cctcgtagca ttacaaaaaa agccccgtag ggcttttttt gtacctgcca atcagctgga
      661 tttaccataa cacccgttgc gtgcaccgcc tgagaggctc tcagggcgtt tctgacggga
      721 aaccggtaaa acaggcaaca aaccaccaga aaacccgcta gaaacgcgcc tgataaattt
      781 taacgccatg catgactatt caccagaatg acggaattct gttttcactt agaaatgata
      841 accagacagg gaaaaacaca cgtgaaccgt caggaatctg ccgctctcaa catggctaaa
      901 tttatccgcg cccagacgct gcttttgctg gaaaaaatcg accagctcga ccttgatgac
      961 gaagcgacag actgtgaaaa attacacgaa caggcagaaa aactttatca gaaactccag
     1021 gcaagactgg actcagacat aacccagtag cttttcgatc gcctccagaa tctccataaa
     1081 ctcgtctttt gaagaatcac cgctctgcag acgtcgctca aggatatcaa taacagagaa
     1141 catcgagaca acacgctcct gtacaagcaa ctcaaccaca gcatgaccga tataccattc
     1201 agcatttgaa ctcacggcaa ctcatactgg aagcggtgaa cggacacgaa atttattgcg
     1261 agtccgtgaa gggcttgcgg ggtgtcgggg cgcagccctg acagaaaatt agtcatactc
     1321 cgaaagcgca gtagaaaaaa ggcaaaacct gctctggagt acagtcagaa gaacggaaaa
     1381 aaaaccgggc ggtaagcccg gtaagtcaag ctagattaga acactcttca gttacatagt
     1441 gcatgttaca acgaccatca tccatgacgg ccgcatgaca aagagtatgg ttcaaaaatc
     1501 agaaaacact cagccggtga catatttaag gggtcggttc cggctgaggg cgaaatgaca
     1561 ccctaagcgt tagctctgtg tcgttgcacg atgtcagcga cggtattctt gctgataccg
     1621 agctcgcgtg cgatccagcg atagctgcgt ccctcggccc tcatcgcaac caccttaggc
     1681 aaaagtcggt ctgattttgg tcgcactccg gcctgacgac caagcctctt accacgtgcc
     1741 ttcgcaacag caaggcctga cttgacccgc tcgctgatga gatcccgctc aaactccgca
     1801 atgccggaaa gaaacgtcgc cagcattcgt ccatacggcg acgaaagatc gaacgccatt
     1861 ccattcatgg ctatcacgga aaccttccag ttctccagtt cacgtagcgt attgagcaga
     1921 tcgagcgtcg agcgccccca ccgggaaagc tcagtgacca ggattgcatc aatttgtctg
     1981 gactgggcaa gcgccaggac tttctttcgc tcggcccggt cgagtttagt tcctgaacct
     2041 gtttccttaa atattcccac cacgtcgtag ccggcacggc cggcgaaggc tcgcagatca
     2101 aattcctggc gttcacaaga ctgatccgct gttgaaaccc ggcagtaaat ggcggcacga
     2161 tgtcccaatt gaaccctcct ggatttttgt atcggaacgc cctgatttat atgggctggc
     2221 tgttgtccaa aacagactat acttcaaaag ggacgaattt gtatgtcacg acgccatatt
     2281 ttcaccgaac ggcagcgagc agcgctgttc gatctgccca cggacgaact gtcgctactg
     2341 aagttctaca cgctgggcga tgatgacctg gaaaacatta ggcagcgccg cagaccggaa
     2401 aacaggattg gctttgccct gcaactttgt gccttacgat atccgggccg tgcactggct
     2461 cctggtgaga tgatcccgcg tgaaatcctt tccttcgtcg gtgctcagct tggagttccg
     2521 gctgatgcgc ttctcactta tgccacacgg cgccaaaccc gtcagcagca catggacacg
     2581 ctgcgcgaaa tttacggcta caagaccttc acgggccgtg gtgcccgtga tctgcgggag
     2641 tggactttcg gccaggccga agatgccaga tcaaacgagg atcttgctca tcgttttatt
     2701 gtgcggtgtc gggaaacttc caccattctg cccgcagtat cgacaatcga gcgcttgtgc
     2761 gcggatgctc tggtcgccgc tgagcggcgg attgaaacgc ggattgtgga aaatttaaca
     2821 gcggatgttc gcgatcacct ggacaaactt ctgagtgaaa tgctcgccgg caatatcagt
     2881 cgtttcatct ggcttcgcaa cttcgaggtt ggtaacaact cggctgctgc taaccgtttg
     2941 ctcgacaggc tcgaatttct gcgtaccctg aatatcaatc atagtgcttt ggccagcata
     3001 cctgcccatc gcattgcccg gctgcgtcgg cagggtgaac gctacttcac cgacggtttg
     3061 cgtgacatca cttcggaccg ccgctgggcg atccttgccg tctgtgttgt ggagtgggaa
     3121 gcggcgattg ctgatgccat agtcgaaacc catgacagga tcgtaggaaa aacctggcgg
     3181 gaagcgaagc gccagcatga cgaaacaatt tccggctcta aagccacact cgcggatacg
     3241 atccgtacct tcaccgcgct gggagcttcg ttgcttgagg cccgcagtga cggaaccccg
     3301 ctggagatgg ctgtcgccag ttcggttgca tgggaccggc tcgctcaact ggtagcgaca
     3361 gggactcaac tcagcaacac gctagccgat gagcctcttg catatgtcgg gcagggatac
     3421 catcgctttc gtcgttatgc gccccgcatg ttgcgctgtc tgaagctcga agccgcgccg
     3481 gtcgccggac cattggtagc agcagctttg tcgatcggag agatgaaagg tgttgcatcg
     3541 ccagaaaggc gtttcctgcg gcccagctcc aaatggaacc gtcatttacg agctcaggaa
     3601 aaaggagata cccgtctttg ggaagtggcg gtactctttc acctccggga tgcttttcgt
     3661 tccggagatg tctggctcgc tcattcgcgc cgctatggtg acctcaagca ggtactggtg
     3721 ccgatgatcg cggcgcagga aaatgcaaaa ctggccgtgc cttccaaccc acaggattgg
     3781 ctggcagaca gaaaggcgcg actcacgatc gctcttaagc ggctggcccg ggctgcccgt
     3841 aacggcacta ttccgcacgg tagcatagaa gatggaacgt tgcggatcga caggttgaca
     3901 gcagacgtgc cggatggtgc cgaggcactc atactggatc tgtatcgccg aatgccgtcc
     3961 gttcggatta ccgacatgct gcttgaagtt gatgcagccc ttggtttcac agatgcgttt
     4021 acccatctga gaaccggggc tccatgtcgc gaccggatcg gtctgctcaa cgtcctgctc
     4081 gctgaagggc tcaatctggg cctgcgtaag atggcggaag ctacaaacac gcatgattac
     4141 tggcagctct cacgccttgc ccgctggcat gttgaaagcg aagccatgaa ccaggcattg
     4201 gcaattgtgg tggccgcgca gggtaaactg ccgatgtcac gcgtctgggg gatgggcacg
     4261 tcagcatcga gcgatggtca gtttttcccg acagcgcggc atggcgaagc catgaacatg
     4321 gtcaatgcca aatatggttc tgttcccggc ctcaaagcgt atactcacgt aagcgaccag
     4381 ttcgcgccat tcgcttgtca gtcgatcccg gcgaccgtga gcgaggcacc gtatattctc
     4441 gatggactac tgatgaacga ggtcggtcgc catgttcgcg aacagtatgc cgatacagca
     4501 ggattcaccg accatttgtt cggagccagt agcctgctcg gctacaatct cgttctgcga
     4561 atcagggatc tgccatcgaa gcggttgtac gtatttaatc ccgatacgac ccccagggag
     4621 ttacgcaagt tggtaggtgg aaaagcccgg gaggatctta tcgttgcgaa ctggcctgat
     4681 attttccgtt gtgccgcgac gatgaccgct ggcaaaatca ggcccagcca actcctgcgc
     4741 aagctcgctt cttacccacg acaaaacaac cttgcagttg cgcttcgtga agttggtcgt
     4801 attgaacgga cccttttcat tattgagtgg atcctggata cggacatgca gcggcgtgct
     4861 cagatcggtc ttaacaaggg agaggcccac catgcgctca aaaatgcgct ccgtatcggg
     4921 aggcaggggg aaattcgcga tcgcacgaca gaggggcagc actaccgaat cgctgggctc
     4981 aatttattga ctgcggtgat catttactgg aataccgtcc atcttggtca tgccgtcacg
     5041 gagcggcgga acgaagggtt ggatgttccc cctgaatttc ttccccacat atccccattg
     5101 ggctgggcgc acattctact gactggcgaa tatctttggc ccaaggaacc gaaagcttag
     5161 ggtgtcattt cgccctcagc cggaaccgac ccctatttaa tacgaactga ttcaaggagc
     5221 gccagcatgc actccctgac acagggatct gtctcggata cggccagata ataagcatcc
     5281 agcatcatct taccggagtc tcccccggac tggcgtaagc agtcagaaat aacagaaaca
     5341 accagctgcc gttcagcatc actcatattc ataaggattc cagaggaaaa accaaacaag
     5401 taaacatcag ttaacggcag cagaaagaaa atattgacag tttagcagtg cgaaacacaa
     5461 aagacggaac ttcgcaggtt tcggggcgca gccctgaacc agtcacatag cgctagcgga
     5521 gtgtatactg gctcaatatg ttacggcgga gtaacattta atgaaagtgc ttcatgtggc
     5581 aggggaaaat gcggctgcgg tgcgtaagtg cgaaatgcag gtggcgatga aatgacgcct
     5641 cctcgctcac tcggtcgctg cgctcctgcc gtgaggctgc ggcgggcgtt accggctcac
     5701 gaatagcggg atcaagagaa ggcgctcaaa tcaggaagga cggggaaaag gatgcggcgt
     5761 tgccgttttt ccataggctc cgcccccctg acaagcatca cgaaatctga cgctcaaatc
     5821 agtggcggcg aaacccgaca ggactataaa gatcccaggc gtttccccct ggtagctccc
     5881 tcgtgcgctc tcctgttcct gcctttcggt ttaccggtgt cattccgctg ttatggccgc
     5941 gtttatctca ttccacgcct gacactcagt tccgggtagg cagttcgctc caagctggac
     6001 tgtatgcacg aaccccccgt tcagtccgac taccacgccc gttccggtaa ctatcaactt
     6061 gagtccaacc cggaaagaca cgacaaatcg ccagtggcgg tagccattgg taacggattt
     6121 agaggagtta gtcttgaagt tatgcgcctg ttaaggctaa actgaaagga cagatttggt
     6181 tactgcgctc ctccaagcca gttaccgcgg ttcaaagagt tggtagctct gagaaccttc
     6241 gaaaaaccgc cttgcagggc ggttttttcg tttccagagc aagagattac gacgcaacgg
     6301 acaggatctc aagaagatca tctgtgatat tcgacagata tgggataaag gattgcaacg
     6361 ccaagagtat atgagacata gcagcagcca cca
//
