LOCUS       NZ_CP084667             4105 bp    DNA     linear   CON 17-NOV-2023
DEFINITION  UNVERIFIED_ORG: Hafnia paralvei strain FDAARGOS_1502 plasmid
            unnamed3.
ACCESSION   NZ_CP084667
VERSION     NZ_CP084667.1
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 4105)
  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  JOURNAL   Unpublished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 4105)
  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
            CP084667.1.
            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/
FEATURES             Location/Qualifiers
     source          1..4105
                     /organism="Hafnia paralvei"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_1502"
                     /culture_collection="DSM:24119"
                     /db_xref="taxon:546367"
                     /plasmid="unnamed3"
                     /geo_loc_name="Germany: Braunschweig"
                     /collected_by="DSMZ"
     gene            50..193
                     /locus_tag="LA328_RS22405"
     CDS             50..193
                     /locus_tag="LA328_RS22405"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001326446.1"
                     /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_072034107.1"
                     /translation="MHEPPVQSDCCALSGNYHLESNPERHDKTPLAAATGNGFAEQRSV
                     EV"
                     /name="replication initiation protein"
     gene            428..1468
                     /locus_tag="LA328_RS22270"
                     /old_locus_tag="LA328_22270"
     CDS             428..1468
                     /locus_tag="LA328_RS22270"
                     /old_locus_tag="LA328_22270"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052606.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RnlA family toxin"
                     /protein_id="WP_047502540.1"
                     /translation="MAQNPFKALNINTDKIEAALTQNGVTNFSSTVKNERETHLSGTYK
                     EIDFLIKLMPSGGNTTIGKASGQNNTYFDEIAGIIKENCLYSDKKTFEYTIPRFSDENK
                     EMLFSFLAEENVKIEEDQNNDPNCKHQYIMTTGNGDRVRAKIYNRGSIQFQGKYLQIAS
                     LINDFMCTILDMKDIIKQKNQEFNVDIKKETIESELHSKLPKSIDQIHDDIKKQLSCSL
                     IMKKIDVEMEDYSTYCFSALRSVEGFIYQLLGSICNPSSSRNLGEYFTENNPKYIIRDI
                     HQETINGEIAEVLCECYTYWHENRHGLFHMKPGVADTKTIDKAESIEIIDTVCQLIDNG
                     IARLKS"
                     /name="type II toxin-antitoxin system RnlA family toxin"
     gene            1465..1845
                     /locus_tag="LA328_RS22275"
                     /old_locus_tag="LA328_22275"
     CDS             1465..1845
                     /locus_tag="LA328_RS22275"
                     /old_locus_tag="LA328_22275"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052605.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RnlB family
                     antitoxin"
                     /protein_id="WP_047502545.1"
                     /translation="MKINKKYQIEVMKDKDKTLFIVYATDIYSPSEFFSKIESDLKKKK
                     VGGDVFFDLIIPNGGKKDRYVYTSFNGERLTSYILNKVTETDEYKSLSERSASFFKKNF
                     DKINANLLSKATSFALKQGIPI"
                     /name="type II toxin-antitoxin system RnlB family
                     antitoxin"
     gene            complement(2054..2539)
                     /locus_tag="LA328_RS22280"
                     /old_locus_tag="LA328_22280"
     CDS             complement(2054..2539)
                     /locus_tag="LA328_RS22280"
                     /old_locus_tag="LA328_22280"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016246513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_226229144.1"
                     /translation="MSFTVAAAENNDNVTYTKPSAGRDLYLTCKGYQLKGASVINVERP
                     SYLEGTGEQVEFAIISLGGASDGLKVFFDSWGFSSFGLIESYVMHEHWSLVHVGGRISV
                     KGEKIDYSFVDNQPQEGGSYKPKTGVFLYGCMNSDKRPSWVEKIYTRTGVFRGGIED"
                     /name="hypothetical protein"
     gene            complement(2716..2925)
                     /locus_tag="LA328_RS22285"
                     /old_locus_tag="LA328_22285"
     CDS             complement(2716..2925)
                     /locus_tag="LA328_RS22285"
                     /old_locus_tag="LA328_22285"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014538403.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_072034108.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENSFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2929..3414)
                     /locus_tag="LA328_RS22290"
                     /old_locus_tag="LA328_22290"
     CDS             complement(2929..3414)
                     /locus_tag="LA328_RS22290"
                     /old_locus_tag="LA328_22290"
                     /inference="COORDINATES: protein motif:HMM:NF016710.3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_072034109.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQTTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMLRMVSQTWLTIVLVSALLIASSAGILWWQGQQIL
                     ENYTTIREQKSTQAMLSERNSGVQLSTCGEQRRRCVRVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            complement(<3449..3883)
                     /locus_tag="LA328_RS22295"
                     /old_locus_tag="LA328_22295"
                     /pseudo=""
     CDS             complement(<3449..3883)
                     /locus_tag="LA328_RS22295"
                     /old_locus_tag="LA328_22295"
                     /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            3812..>4105
                     /locus_tag="LA328_RS22300"
                     /old_locus_tag="LA328_22300"
                     /pseudo=""
     CDS             3812..>4105
                     /locus_tag="LA328_RS22300"
                     /old_locus_tag="LA328_22300"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="incomplete; too short partial abutting assembly gap;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: GeneMarkS-2+."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     Typing          complement(2..139)
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.683"
                     /coverage="85.0"
                     /evalue="8.75e-56"
     Typing          complement(2619..4102)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.929"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 acgcctgaca ctcagttccg ggtaggcagt tcgctccaag ctggactgta tgcacgaacc
       61 ccccgttcag tccgactgct gcgccttgtc cggtaactat catcttgagt ccaacccgga
      121 gaggcacgac aaaacgccac tggcagcagc cactggtaac ggattcgcag aacaaagaag
      181 tgttgaagtg tgaggtgaag tacagctaca ctgtaataac gaatttggtt tctgtgctct
      241 gcgaaagcca gttacctcgg ttcaaagagt tggtagctca gcgaaccttg agaaaaccac
      301 cgttggtagc ggtggttttt tctttatgcg atgatgaatc aatcagccta tcaagtcaac
      361 gaaccgcgct tccattgaca aaaaaacaag atctgtacat attcagaaaa aacaacggat
      421 tgaggcaatg gcacagaacc catttaaagc actaaatatc aatacagaca agattgaagc
      481 tgctctgacg cagaatggcg tcacaaactt ttcttctacc gtgaaaaacg aaagagagac
      541 gcatttatca gggacatata aagaaataga ttttttaata aagctaatgc catcaggtgg
      601 aaacaccact ataggaaagg catcagggca aaacaatact tactttgatg agatcgctgg
      661 cattataaaa gaaaattgtt tgtattcaga taaaaaaact tttgaataca ccatcccaag
      721 attcagcgat gaaaataagg aaatgttatt ttcatttctt gctgaagaaa acgtaaaaat
      781 agaagaagat caaaacaacg atcctaactg caagcatcaa tacatcatga ccactggtaa
      841 tggtgacaga gtcagagcga aaatttacaa ccgtggttca attcaattcc aaggaaaata
      901 tcttcaaatc gcaagtttga ttaatgattt catgtgcacc atactggaca tgaaagatat
      961 tataaaacag aagaatcaag aatttaatgt tgacataaaa aaagaaacaa ttgagtcaga
     1021 attacatagt aaactcccaa aaagcatcga ccaaatccat gacgacatca aaaaacagct
     1081 atcctgctcg ctcataatga aaaaaataga tgtcgaaatg gaagattact caacgtattg
     1141 tttctcagct ttaagatctg tggaaggctt tatatatcag ctacttggaa gtatatgcaa
     1201 tccatcatca tcaagaaatc ttggcgagta ctttactgag aataacccga aatacataat
     1261 aagagatata caccaagaaa ctattaatgg tgaaatagca gaagttttgt gtgagtgcta
     1321 cacttactgg catgaaaaca gacatggttt gttccatatg aaaccaggtg tggctgacac
     1381 taagacaatt gacaaagcag aatctattga aattatcgat actgtatgtc agttgataga
     1441 taacggcata gctaggttga aatcatgaaa ataaacaaaa aatatcaaat agaggtgatg
     1501 aaggataaag ataaaacttt attcattgtc tacgctacag atatttacag cccgagcgaa
     1561 tttttctcta aaatcgagtc tgatttaaag aaaaagaaag ttgggggcga tgtttttttt
     1621 gatttaataa ttcctaatgg tggaaaaaaa gaccgttacg tctatacatc attcaatggc
     1681 gaacgattaa caagctacat attaaacaaa gttacggaaa cagatgagta taaatcctta
     1741 tctgaacgct cagcttcgtt ctttaaaaaa aactttgata agattaatgc aaaccttcta
     1801 tctaaagcca catcgtttgc tttaaaacaa ggcattccaa tataaaagca attgcagaat
     1861 tgaacataac atgccttggg cgcaccgccg cagacggcct cagcgccgtt ctgcgccctg
     1921 aaccgcaaaa gagcacctct taccacgcga aaacgccgca aaagagcccc cgtaagttct
     1981 tacggtatgc atagccatgc acgaaaatga actgacactc tgttcaatag attttcatgc
     2041 tgtacgcagt attttagtct tctatgcccc ctcgaaacac gcctgttctt gtgtagattt
     2101 tttcgaccca agatggcctt ttatccgagt tcatgcagcc gtacaggaac acacctgttt
     2161 tgggtttata gctcccaccc tcctgtggct ggttatctac aaatgaataa tcaatctttt
     2221 cacccttgac tgaaatacgc cccccaacat gaactaaaga ccagtgctca tgcatcacat
     2281 aactttcaat caatccaaaa gaagaaaaac cccatgaatc aaaaaaaacc ttgagtccat
     2341 cagatgcacc acctagagaa atgattgcaa attcaacctg ctcacctgta ccttcaaggt
     2401 aagaaggtct ctcgacgtta attacagatg cacccttcag ctgataacct ttacaggtaa
     2461 gatataagtc cctcccggct gacggttttg tgtatgtaac gttgtcgtta ttctccgcag
     2521 cagcgactgt aaatgacata gccaaaacca ctgagactga gcaagcccag aaacacttca
     2581 taacgtatcc cttttcatcg attaactaca ttccaagctc aaaacctttc tgccgctgcg
     2641 atcgttccag ctccagcgct ttctggtgct gcgccgcccg ctcctgttcc aggcgtgcct
     2701 ctatcccgtt aagcttcacg acaaccggcg cagctgctcg ctcaaactct gcacctgcct
     2761 gctcaagccc gtgacgcgct cgctcagcgc cgcgttctcc cgttgcataa gaccagacat
     2821 cgtccgccat tccgcgaagg agttctccca ctcgtccagc cttttcgagt agtcctgctg
     2881 tagctgctct aatgcgctca gcaactgttt ttccagctcc gtcatgtgct atttccccgc
     2941 cagtatcatc cagctcgaat cctctccgaa ccgtcccgct tccgggttca ccctcacgca
     3001 gcggcgtctc tgctctccgc aggtcgatag ctgtacgccg ctgttcctct ctgacagcat
     3061 ggcctgcgtg ctcttctgct cccggatggt cgtgtagttc tcgagtatct gctgcccctg
     3121 ccaccacaga attcccgcgc tcgaggcgat cagcagcgcg gagaccagca cgatggtcag
     3181 ccacgtctgg ctgaccatgc gcagcatccc tttcgttcgc tggctcatgg ctgaggacag
     3241 cttccggtcg tggtcgagga tggcggcgct gattctcttc tcgctttcgc tcagttccgc
     3301 tctgacagac ttctcgtgct cgctgaatgc ggctttcagc atctcgccgg tagtctgctg
     3361 ctgcgctttc gatttctgct ctaagtcctt cgccagcgtt aaaagactgt tcatagatgg
     3421 ctcccttcag tcggatgttt cgccccccgt ccgggtcggc aatgctgatg ctgctttttg
     3481 tggtgcgcac cacctcaaaa cccgcgcttt ccagcgcctc cgtgacgtcc tgacgggttt
     3541 tcagctcccc ggacgaggct aaggaaagca aaccccgtgt aatcgcctga gcggcttcct
     3601 gcttcgcttc cggcagcgcg gacggcgtga ccagcgcccg ccggttctcc ggcgcgttcg
     3661 ggtcgtgcag ccccagcctg ccgttcacga tggtctgcca ggcatcgatg cgcggacgat
     3721 cggcgcggtc gtaatacggc tgtagccgtt tgccggtcag cagctccgtg ttcgggatca
     3781 ggaagttcag ctccagccgc cccttgtccc ggtgctcaac ccacagcacg ctgtactggt
     3841 ctttatcgag tccgggcatc agaacccgct caaagctcgc catcagcttt tcacgctggc
     3901 cgggcggcaa atcctgttcg gcaaaggaca gcacgccgga ggtgtatttt ttggcgtagg
     3961 gagaggcgtc gataagctcc cggacttcct ccggcttccc ctgcaggacg gtggcgccat
     4021 cgcgctggcg gtcttttccc agcagataat ccaccggacc ggcaccgccg ccgcgccctc
     4081 gcgggtgaaa cttaacgatc atcgt
//
