LOCUS       NZ_CP084666             5113 bp    DNA     circular CON 17-NOV-2023
DEFINITION  UNVERIFIED_ORG: Hafnia paralvei strain FDAARGOS_1502 plasmid
            unnamed2, complete sequence.
ACCESSION   NZ_CP084666
VERSION     NZ_CP084666.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN21218858
            Assembly: GCF_020450285.1
KEYWORDS    UNVERIFIED; UNVERIFIED_ORGANISM; RefSeq.
SOURCE      Hafnia paralvei
  ORGANISM  Hafnia paralvei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Hafniaceae; Hafnia.
REFERENCE   1  (bases 1 to 5113)
  AUTHORS   Sproer,C., Gronow,S., Severitt,S., Schroder,I., Tallon,L.,
            Sadzewicz,L., Zhao,X., Boylan,J., Ott,S., Bowen,H., Vavikolanu,K.,
            Hazen,T., Aluvathingal,J., Nadendla,S., Lowell,S., Myers,T. and
            Yan,Y.
  TITLE     FDA dAtabase for Regulatory Grade micrObial Sequences (FDA-ARGOS):
            Supporting development and validation of Infectious Disease Dx tests
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5113)
  AUTHORS   Sproer,C., Gronow,S., Severitt,S., Schroder,I., Tallon,L.,
            Sadzewicz,L., Zhao,X., Boylan,J., Ott,S., Bowen,H., Vavikolanu,K.,
            Hazen,T., Aluvathingal,J., Nadendla,S., Lowell,S., Myers,T. and
            Yan,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (15-SEP-2021) Center for Devices and Radiological Health,
            US Food and Drug Administration, 10903 New Hampshire Avenue, White
            Oak, MD 20903, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: SMRT v. 9.0.0, HGAP v. 4.0, SPAdes v. 3.14.1
            Genome Coverage                   :: 1507.48x
            Sequencing Technology             :: Pacbio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/17/2023 08:00:19
            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)                     :: 4,464
            CDSs (total)                      :: 4,343
            Genes (coding)                    :: 4,297
            CDSs (with protein)               :: 4,297
            Genes (RNA)                       :: 121
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 46
            CDSs (without protein)            :: 46
            Pseudo Genes (ambiguous residues) :: 0 of 46
            Pseudo Genes (frameshifted)       :: 18 of 46
            Pseudo Genes (incomplete)         :: 31 of 46
            Pseudo Genes (internal stop)      :: 7 of 46
            Pseudo Genes (multiple problems)  :: 8 of 46
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            GenBank staff is unable to verify source organism provided by the
            submitter.
            REFSEQ INFORMATION: The reference sequence is identical to
            CP084666.1.
            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..5113
                     /organism="Hafnia paralvei"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_1502"
                     /culture_collection="DSM:24119"
                     /db_xref="taxon:546367"
                     /plasmid="unnamed2"
                     /geo_loc_name="Germany: Braunschweig"
                     /collected_by="DSMZ"
     gene            join(4774..5113,1..74)
                     /locus_tag="LA328_RS22230"
                     /old_locus_tag="LA328_22230"
     CDS             join(4774..5113,1..74)
                     /locus_tag="LA328_RS22230"
                     /old_locus_tag="LA328_22230"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004846644.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Exc2 family lipoprotein"
                     /protein_id="WP_226229138.1"
                     /translation="MMKALNTVIAVAVFSFSLVGCSQHLSSAERHAKHFVYAEKSDFDP
                     SYQTRMQESARLSVPFFDQFYQQGKKDKLAGVSREQAQQQSDYFSSPAFLDAIQRESEF
                     AGKKYSQSQNQKWRLLMSQEAAGAYLDGYEGRK"
                     /name="Exc2 family lipoprotein"
     gene            493..681
                     /locus_tag="LA328_RS22235"
                     /old_locus_tag="LA328_22235"
     CDS             493..681
                     /locus_tag="LA328_RS22235"
                     /old_locus_tag="LA328_22235"
                     /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_008815949.1"
                     /translation="MSYSTAPVDNGHSTAPLKKSVAVQQQPRPKHVTAGKGVSPEREQG
                     AGKYAFSADSPEQGRVP"
                     /name="hypothetical protein"
     gene            1130..1453
                     /locus_tag="LA328_RS22240"
                     /old_locus_tag="LA328_22240"
     CDS             1130..1453
                     /locus_tag="LA328_RS22240"
                     /old_locus_tag="LA328_22240"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000613379.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_011178376.1"
                     /translation="MSDKRTKMLTLWVTPEEHERLLARCDSPRLATWMREVCLEEKPTR
                     TSKPLPTLAPELLRQLAGMGNNLNQIARRLNSGEWSAHDRVQVVAALMALERELQLLRE
                     QAR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1669..>2121
                     /locus_tag="LA328_RS22385"
                     /pseudo=""
     CDS             1669..>2121
                     /locus_tag="LA328_RS22385"
                     /inference="COORDINATES: protein motif:HMM:NF015397.3"
                     /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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            2669..2866
                     /locus_tag="LA328_RS22255"
                     /old_locus_tag="LA328_22255"
     CDS             2669..2866
                     /locus_tag="LA328_RS22255"
                     /old_locus_tag="LA328_22255"
                     /inference="COORDINATES: protein motif:HMM:NF016769.3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD/MobD family mobilization/exclusion protein"
                     /protein_id="WP_264167299.1"
                     /translation="MQQQAWSESYSALQQMFTTTSAQAETLNAQKIRLSHSLSRLLEQV
                     SDLSGQVQSLSRQVSSIKGR"
                     /name="MbeD/MobD family mobilization/exclusion protein"
     gene            3062..3352
                     /locus_tag="LA328_RS22260"
                     /old_locus_tag="LA328_22260"
     CDS             3062..3352
                     /locus_tag="LA328_RS22260"
                     /old_locus_tag="LA328_22260"
                     /inference="COORDINATES: protein motif:HMM:NF015489.3"
                     /GO_function="GO:0015643 - toxic substance binding
                     [Evidence IEA]"
                     /GO_process="GO:0030153 - bacteriocin immunity [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin E1 family microcin immunity protein"
                     /protein_id="WP_096081283.1"
                     /translation="MAACILYASYGDDEPKIIALRIFGLASAILFPFSRFLIEKAALRY
                     TKKEFWKTGFFKDGVPKTYLMTLYFIFIFMTSIPIGVLSVCFEIKNVTAKI"
                     /name="colicin E1 family microcin immunity protein"
     gene            complement(3369..4595)
                     /locus_tag="LA328_RS22265"
                     /old_locus_tag="LA328_22265"
     CDS             complement(3369..4595)
                     /locus_tag="LA328_RS22265"
                     /old_locus_tag="LA328_22265"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004846643.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_function="GO:0140911 - pore-forming activity [Evidence
                     IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA];
                     GO:0050829 - defense response to Gram-negative bacterium
                     [Evidence IEA]; GO:0031640 - killing of cells of another
                     organism [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin-like pore-forming protein"
                     /protein_id="WP_011178375.1"
                     /translation="MSGGDGKGHNSGAHDSGGSINGTSGKGGPSSGGASDNSGWSSENN
                     PWGGGNSGMIGGSQGGNGANHGGENTSSNYGKDVSRQIGDAIARKEGINPKIFTGYFIR
                     SDGYLIGITPLVSGDAFGVNLGLFNNNQNSSSENKGWNGRNGDGIKNSSQGGWKIKTNE
                     LTSNQVAAAKSVPEPKNSKYYKSMREASDEVINSNLNQGHGVGEAARAERDYREKVKNA
                     INDNSPNVLQDAIKFTADFYKEVFNAYGEKAEKLAKLLADQAKGKKIRNVEDALKSYEK
                     HKANINKKINAKDREAIAKALESMDVEKAAKNISKFSKGLGWVGPAIDITDWFTELYKA
                     VKTDNWRSLYVKTETIAVGLAATHVTALAFSAVLGGPIGILGYGLIMAGVGALVNETIV
                     DEANKVIGI"
                     /name="colicin-like pore-forming protein"
     Typing          1451..2901
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.38"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atcagaaatg gcgattattg atgtcccaag aagccgctgg cgcttatttg gatggctatg
       61 agggacgaaa ataagagggg gattatgttg ttagtgagta agatccgctt gagatccttt
      121 ttagatcgtc gtagtctcct gagcgtaaac gaaaaaaccc gccgaaaggc gggttagttc
      181 ggattcgttg agcttgcaac tcgcggattc gaacggtaac tggacttttg cgggaacagt
      241 caccaaatct gtacagatag tttagcctct agaggccgac tacttcaagt gcaaatgtat
      301 ttatagtgta tttacacctc ccccgcaaac ctccagttac caatggctac cgccagtggc
      361 gaattttttc gtgttctatc cggattggcc tcaagagtat gttgccggat gagcgcggta
      421 gtcgggttga acgggggtat tgctcaaaca acccgagcgt gcgacgcgca ccaaaacctt
      481 gtacggacag gcatgtcgta cagcacagca ccagtggaca acgggcattc aacggcacca
      541 ctaaaaaaaa gcgtggcggt acagcagcag ccaaggccaa agcatgtgac agcaggaaag
      601 ggtgtgtctc cggagcgcga gcaaggggca ggaaaatatg cattttccgc cgatagtccg
      661 gagcaaggcc gagtacctta gacagtgatg tctggggtgg ctcgtcctgt cttgaagggc
      721 accgaaaaga caggacgagg gcggcgagga gcctttttgg cgacatcctt tttatctttc
      781 ttcacatatt cactctctaa acgtttgaga ataatttcac cgctcgccgc aagcgcagac
      841 taggcacgtc cggcttttgt ccggacagct ctgtctgtgc gaggaagcgg aatatcgccc
      901 gcagtccatt taagcacggt cactctgttc ccttttatcg gtatttccat gcgcaatcta
      961 tgctagattc agcacagcac taacatatta agccagtata cactacgcta gcgctacgtg
     1021 actggttcag ggctgcgccc cgaaacccgc gctgacgcgc ctacggcttg tctaaccccg
     1081 aagaaagcca gcataaatgc tgtctccctt cggggttttg gagagggtta tgtctgacaa
     1141 acgcacgaaa atgctcaccc tgtgggtgac tccggaggag cacgagcgtc tacttgctcg
     1201 atgtgattcg ccgcgactgg cgacatggat gagagaggta tgcctcgagg aaaaacccac
     1261 ccgaacatca aaacctttgc ctacgttggc gccagaactg ctgcgacagc ttgcgggtat
     1321 gggcaacaat ctaaaccaga tagcgcggcg gctgaatagc ggtgagtggt cagcacatga
     1381 ccgtgttcag gtggtcgctg ccctgatggc gttagagcgc gagctgcaac ttcttcggga
     1441 gcaggcgaga tgattgtaaa atttcacgcc agagggacag gaaagggctc aggaccggtt
     1501 gattaccttc tgggtaagga tagggctaga gttgatgcaa aattgcttag aggggcttct
     1561 gaggaggtta tagctctcat tgatagtagc ccgtatgcga agaaatatac ctccggcgtg
     1621 ttgtcgtttg ctgaggctga tttggcttcg gagacaaagc agaaagtgat ggacagtttt
     1681 gagcgtgcgc ttttgcctgg tctggatgct gaccaatatt cggtgttgtg ggtagagcat
     1741 cgagacaaag ggcgtttgga gcttaatttt gtaataccga acatcgaatt acagcgcggt
     1801 aagcgtctcc aaccgtactt tgaccgtgct gaccgtccgc gcatcgatgc gtggcaaacg
     1861 gtggtgaatg cgcaattagg attacatgac ccgaatgacc cgctcaatca gcgggcgttg
     1921 gtgacggcga acagtttgcc tcgagagaaa caggcggccg cagaggcgat tacacatggt
     1981 ttgctgcgac gtattgatgc aggagaaata aaaaatcgag ctgatgttgt tgaggcgctt
     2041 agagatgcgg gtttttcggt ggtcagacag gcaaaaaaca gtatcagtct cgcgtcgcca
     2101 gatggtgggc aaaatcttcg gttaaagggg gctatctatg gacaagattt tcgatttagc
     2161 gaaggacttc gagcagaaat cgacaaagca ggcgagcact atcgaagcga atctcgcgca
     2221 cgtgttcaaa acgcacgaga acgctatcaa tacggcgttg cactcaagcg ggcagagaat
     2281 cagcagcgct atccaagagc agagcttaac gatgcgttgg atggtgttga aaagctggtt
     2341 atcgataggg gttggtctgt tggtgatgtt gtgtctgggc gggagcgtgc tgtggtggca
     2401 agggacacag atacgggaga acgcgcagtt gatgacagaa cagtcggata cgttgaaaaa
     2461 gttgaacacg aagacgtggg gcattcggtt tcaagaggat acgagcggtc gctttttggt
     2521 gttaccgaag ggcgtgaaag cgaacccgaa ctggacgttc gaggacggga cacggcaggg
     2581 tgtcaaattg gagaggaagt aaatacagat gacagcatta gagcaggaat tattgagcgc
     2641 cttcgaggcg ttacagcaga gttacgtgat gcagcaacaa gcgtggtcgg aaagctacag
     2701 cgcgttgcag cagatgttca cgactacttc cgcacaggcg gaaaccttga acgcgcagaa
     2761 aatccgcttg tctcatagtc tgagcaggtt gctcgagcag gtaagcgact tgagtggtca
     2821 ggtgcagagc ttaagcaggc aagtgtcgag tatcaaaggc agataaggcg tgatagtccg
     2881 cggtttaagg ggctagaatt ataatcagat gaatagtgga acgtcgtcgt tagtggggat
     2941 gggaaacttt taattgggcg tttctccggt gttgagaacg ttattttacc aaatgtaaaa
     3001 ctttgtgagg gattttatga caaggaaata ttacatacat aatatgtttt ggggatactt
     3061 tatggctgct tgtattcttt acgccagtta tggtgatgac gaacctaaaa taattgcgct
     3121 cagaatcttt ggtttggcta gcgctattct atttcctttc tctcggtttc taatagagaa
     3181 agcagcgctt agatatacga aaaaagaatt ttggaaaaca ggttttttta aggatggtgt
     3241 gccaaaaaca tatttaatga ctttgtattt tatttttatt tttatgacat caattcctat
     3301 tggtgttctt tctgtttgtt ttgaaataaa aaatgtgacc gctaaaatat agcggtcata
     3361 caatcaagtt aaatcccaat gaccttattt gcctcgtcaa ctattgtctc gttaactaac
     3421 gccccaaccc cagccataat caaaccataa cctaaaatac ctataggccc acccaagaca
     3481 gcactgaatg ctaaggcggt gacatgggtt gcagctagcc ctactgcaat agtttcagtt
     3541 ttaacataaa gagatctcca attatcagtt ttcactgctt tgtataattc tgtaaaccaa
     3601 tcagttatat cgatagctgg gccaacccaa cctagtcctt tgctgaactt ggatatattt
     3661 tttgcggctt tttctacatc catagactcc aaagccttgg cgatagcttc gcgatctttc
     3721 gcattgattt ttttgttaat gttagccttg tgtttttcat aagatttcaa tgcatcttct
     3781 acattgcgga tctttttacc tttagcttga tcagctaata acttggctag tttttcggct
     3841 ttttctccgt aagcgttaaa aacttcctta taaaaatctg ctgtaaattt aatagcatcc
     3901 tgtagcacat tgggactatt atcattgatt gcgttcttta ctttttctct gtaatctctt
     3961 tcagctctag ctgcctcacc aactccatgc ccttggttta aattagaatt aataacctca
     4021 tcgctagctt ctctcatgga cttataatat ttactatttt taggttctgg aacggattta
     4081 gcagcagcta cttggtttga agtaagttca ttagttttaa tcttccatcc accttggcta
     4141 ctatttttaa tgccatctcc attccttcca ttccatccct tattttcact actactattt
     4201 tgattgttat tgaacaggcc aagattaacg ccaaaggcat caccactgac aagtggcgtt
     4261 attccgatca aatatccatc tgaacggata aagtacccag tgaatatttt cggattgatg
     4321 ccttcctttc tggctatcgc atcaccgatt tggcgtgata catctttccc atagttagaa
     4381 gatgtatttt cgccaccatg attagctccg ttacctcctt gactgccacc aatcattccc
     4441 gagttaccac cgccccacgg gttattttcc gaactccacc cagaattatc tgatgctcct
     4501 ccgcttgatg gcccaccttt cccagaagtt ccattaatgc tgccaccgga atcatgtgct
     4561 ccactattgt gacccttgcc atctccacca ctcataatat tgccctctct gacgttagat
     4621 aaaaagtata aaatactgta tataaataca ttgttatata tacagtattt tgatcttatg
     4681 cctgactttt aacaaagtca ataacggtag gtatgcaaaa taattacttc gctaatgcta
     4741 tgatgaaaat ggtttttttt taaaaagagg cttatgatga aagcattgaa tactgtgata
     4801 gctgtcgctg ttttttcttt tagtttggtg ggctgttctc aacatctgtc gagtgcagaa
     4861 cggcatgcga aacacttcgt atatgcagaa aaaagtgatt ttgacccaag ttatcaaacc
     4921 cgaatgcagg agagtgctag gttatcagtg cccttttttg accagtttta ccaacaaggt
     4981 aagaaggata agctcgctgg agtaagtcgc gagcaagcac aacagcaatc ggattatttt
     5041 tctagcccag cgtttctaga cgctatccaa cgggaaagtg aattcgcagg taaaaagtat
     5101 agtcagtcac aaa
//
