LOCUS       NC_006840               5514 bp    DNA     linear   CON 10-MAR-2020
DEFINITION  Aliivibrio fischeri ES114 chromosome I, complete sequence.
ACCESSION   NC_006840
VERSION     NC_006840.2
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN02604303
            Assembly: GCF_000011805.1
KEYWORDS    RefSeq.
SOURCE      Aliivibrio fischeri ES114
  ORGANISM  Aliivibrio fischeri ES114
            Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales;
            Vibrionaceae; Aliivibrio.
REFERENCE   1  (bases 1 to 5514)
  AUTHORS   Mandel,M.J., Stabb,E.V. and Ruby,E.G.
  TITLE     Comparative genomics-based investigation of resequencing targets in
            Vibrio fischeri: focus on point miscalls and artefactual expansions
  JOURNAL   BMC Genomics 9, 138 (2008)
   PUBMED   18366731
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 5514)
  AUTHORS   Ruby,E.G., Urbanowski,M., Campbell,J., Dunn,A., Faini,M.,
            Gunsalus,R., Lostroh,P., Lupp,C., McCann,J., Millikan,D.,
            Schaefer,A., Stabb,E., Stevens,A., Visick,K., Whistler,C. and
            Greenberg,E.P.
  TITLE     Complete genome sequence of Vibrio fischeri: a symbiotic bacterium
            with pathogenic congeners
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 102 (8), 3004-3009 (2005)
   PUBMED   15703294
REFERENCE   3  (bases 1 to 5514)
  AUTHORS   Mandel,M.J., Stabb,E.V. and Ruby,E.G.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-OCT-2007) Department of Medical Microbiology and
            Immunology, University of Wisconsin School of Medicine and Public
            Health, 1550 Linden Drive, Madison, WI 53706-1521, USA
  REMARK    Sequence update by submitter
REFERENCE   4  (bases 1 to 5514)
  AUTHORS   Ruby,E.G., Urbanowski,M., Campbell,J.W., Dunn,A., Faini,M.A.,
            Gunsalus,R.P., Lostroh,P., Lupp,C., McCann,J.R., Millikan,D.S.,
            Schaefer,A.L., Stabb,E.V., Stevens,A.M., Visick,K.L., Whistler,C.A.
            and Greenberg,E.P.
  TITLE     Direct Submission
  JOURNAL   Submitted (16-SEP-2004) Kewalo Marine Laboratory, and W.M. Keck
            Microbial Communities and Cell Signaling Program, University of
            Hawaii, Honolulu, HI 96081, USA
COMMENT     ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 03/10/2020 07:52:53
            Annotation Pipeline               :: NCBI Prokaryotic Genome
            Annotation Method                 :: Best-placed reference protein
            Annotation Software revision      :: 4.11
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA;
            Genes (total)                     :: 3,941
            CDSs (total)                      :: 3,781
            Genes (coding)                    :: 3,731
            CDSs (with protein)               :: 3,731
            Genes (RNA)                       :: 160
            rRNAs                             :: 13, 12, 12 (5S, 16S, 23S)
            complete rRNAs                    :: 13, 12, 12 (5S, 16S, 23S)
            tRNAs                             :: 119
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 50
            CDSs (without protein)            :: 50
            Pseudo Genes (ambiguous residues) :: 0 of 50
            Pseudo Genes (frameshifted)       :: 38 of 50
            Pseudo Genes (incomplete)         :: 7 of 50
            Pseudo Genes (internal stop)      :: 13 of 50
            Pseudo Genes (multiple problems)  :: 7 of 50
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence was derived from
            CP000020.
            On Apr 4, 2008 this sequence version replaced NC_006840.1.
            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/
            Annotation Pipeline (PGAP)
            set; GeneMarkS-2+
            repeat_region
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..5514
                     /organism="Aliivibrio fischeri ES114"
                     /mol_type="genomic DNA"
                     /strain="ES114"
                     /db_xref="taxon:312309"
                     /chromosome="I"
     gene            1..1356
                     /locus_tag="VF_RS03140"
                     /old_locus_tag="VF0603"
                     /old_locus_tag="VF_0603"
     CDS             1..1356
                     /locus_tag="VF_RS03140"
                     /old_locus_tag="VF0603"
                     /old_locus_tag="VF_0603"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017018649.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="gnl|TC-DB|Q72XQ0|4.A.3.2.8"
                     /protein_id="WP_011261349.1"
                     /translation="MGTQAVNLQSTIMEKVNKFLPKILKVVNSKPIVAIKEGFMLTMPL
                     TIIGSVFLLLAFVPIDGYNEFMAGIFGAEWSTPLFQVVGATFDILALIGAFGIAYTYVK
                     YEGHNGVNAGVLAIVSLLIVMNAFVVAPDGVTQIGGVIPKAFLGGKGMIAAIVIGLVVG
                     IIYSMAFNRNWVIKLPDSVPEGVSNAFKSLIPGFLIITLAFLTYIFFEVVFERTFIETI
                     YHIIQTPLQSMSDSFFGAVGIALLISLLWWCGVHGPVIVMGIMGPIVTANALHNQSIVN
                     AGEALIAGENGKVVTNQFVDQFITVGGSGLTFGLVCCMVLFARSIQFKQLGRLSFIPGI
                     FNINEPVIFATPIIFNPIMFIPFVTAPVLSAIMVYTSINMGFVGPFTAVQVPWTTPMVL
                     SGFIVGGWSAALLQIAVFCMTVCVYFPFFKYQDKLAAQDEAKAAAPTSQATA"
     gene            1389..1694
                     /locus_tag="VF_RS03145"
                     /old_locus_tag="VF0604"
                     /old_locus_tag="VF_0604"
     CDS             1389..1694
                     /locus_tag="VF_RS03145"
                     /old_locus_tag="VF0604"
                     /old_locus_tag="VF_0604"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005417897.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="gnl|TC-DB|Q9KSH5|4.A.3.2.6"
                     /protein_id="WP_005417897.1"
                     /translation="MKKILLLCAAGMSTSMVVKKMRESAEQKGLDIHIEAHGVETIQDY
                     LSEYDLFLLGPQIRFKKDELQKLADEVNKKVEVIDMMDYGMMKGEKILNDALALLD"
     gene            1734..3143
                     /locus_tag="VF_RS03150"
                     /old_locus_tag="VF0605"
                     /old_locus_tag="VF_0605"
     CDS             1734..3143
                     /locus_tag="VF_RS03150"
                     /old_locus_tag="VF0605"
                     /old_locus_tag="VF_0605"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005417898.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="GH1"
                     /protein_id="WP_005417898.1"
                     /translation="MKFAHDFLFGAATASYQVEGAWDQDGKGPTNWDEFTKIPGKTFEG
                     TNGDVAVDHYNRYKEDIALMAEMGLESYRFSISWARIFPNGTGEINQKGIDFYNNLIDE
                     CLKYGIVPFVTLYHWDLPLALEKEGAWLNKATGDAYVEFAKLCFNEFGDRVKHFITFNE
                     TVVFCALGYMAGAHPPGIQNDPKKYFQATHNVFYAHAKAVIEYKKLNQFGEIGLSHVFS
                     PAFGVDDSEESHFAAMHANQFSMNWFYDPILLGKYPEYVVKQLQEEGNLPDWTDEELQT
                     IFEAAPLNDFMGLNYYQPQRVEKIQGDVEARTITRENSTGSPGNPSYDNVYRTVKMADK
                     KYTKWDWEISPEGFVGGLEMLKEHYGQIKLYITENGLGDEDPIIEGEVCDIPRINFIKE
                     HLGAVKEAVRRGVHIKGYYAWSAIDLLSWLNGYKKQYGFIYVDHQNGLARKKKASFHWF
                     KDVIATRGEDI"
     gene            3170..4105
                     /locus_tag="VF_RS03155"
                     /old_locus_tag="VF0606"
                     /old_locus_tag="VF_0606"
     CDS             3170..4105
                     /locus_tag="VF_RS03155"
                     /old_locus_tag="VF0606"
                     /old_locus_tag="VF_0606"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011261350.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ROK family protein"
                     /protein_id="WP_011261350.1"
                     /translation="MATYISFDIGGTDIKFGVLNEQGKVLEQGKVKTETCGEKIIATLV
                     DIKEQWSKKYTFDGAAFSLPGFVDVNTGYLKTGGAIDDFYGFQFKDELTKKLSLPVELE
                     NDVNCVALAEKWLGKAQHVENFICITIGTGIGGAIYINNQMVRGHGFMAGEFGYMFTRN
                     VFDIEDKATASMSFTASVREGLRRRYSTLKNINSIDNISGKDIFELASTGDEVAIKVID
                     DFYNNIAIGLYNLTFILNPEKIIIGGAISSREDLISNIEKKFNQIIKSQSSINEFNVKE
                     LVSIEKSTFNNDSGLIGAVYHFLTMKNKFK"
     gene            4117..4440
                     /locus_tag="VF_RS03160"
                     /old_locus_tag="VF0607"
                     /old_locus_tag="VF_0607"
     CDS             4117..4440
                     /locus_tag="VF_RS03160"
                     /old_locus_tag="VF0607"
                     /old_locus_tag="VF_0607"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011261351.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="gnl|TC-DB|C4X746|4.A.3.2.7"
                     /protein_id="WP_011261351.1"
                     /translation="MLVGEELETTVMELIINAGESKSCAMEALRAAKSGEWDKVDDLLK
                     QSAEASKRAHDVQTQLIGMDEGEGKVPVNLIMVHAQDHIMTSMLAKEMIQELIEIHRAL
                     QNK"
     gene            4510..5514
                     /locus_tag="VF_RS03165"
                     /old_locus_tag="VF0608"
                     /old_locus_tag="VF_0608"
     CDS             4510..5514
                     /locus_tag="VF_RS03165"
                     /old_locus_tag="VF0608"
                     /old_locus_tag="VF_0608"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017018647.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="STP|LacI,STP|Peripla_BP_3"
                     /protein_id="WP_011261352.1"
                     /translation="MATINDVCKLAGVSKATVSRVMNGKGPVKEETKKLIFDAMETLDY
                     KPSLVAQALATNSSNSIGLIVSFFDGYYFGILLKEATRIAEESGKQLIVTDGHNQVETE
                     IEAINSLVARKCDAILIYSRTMTADDYCEIQKKLPIPLVVINRTLPDGLGHAVAFDQYN
                     ASQMAIEHLVGLGHKNIAIITLNMTSSTGQIRLKGAKETLEKHGIAYDDNLTIIKNGKL
                     EDGYQACKELLKRSQDISAIFCFNDHLALGAIKALKEMNIRVPEDISIVGIDNDEISAF
                     LSPALTTINIPIQKVTQLAMDKALRLISDKEVKATTEILKGNIIVRESTKNIN"
ORIGIN
        1 atgggtactc aagcggtaaa tttgcaaagt actatcatgg aaaaggtgaa taaattccta
       61 cctaaaattt taaaggttgt gaattcaaaa ccgatcgtag cgattaaaga aggcttcatg
      121 ttaacaatgc cattgaccat tataggttca gtgtttttgt tattggcgtt tgtacctatt
      181 gatggttaca acgagtttat ggctggaatt tttggagcag aatggtcaac accattgttt
      241 caagttgtag gggcaacatt tgatattttg gcactaattg gtgcttttgg tattgcgtat
      301 acttacgtta aatatgaagg acataatggt gtaaatgcgg gggtattagc cattgtttct
      361 cttcttattg taatgaatgc ctttgttgtc gcacctgatg gtgtaactca aattggtggc
      421 gtaataccga aagcctttct tggtggtaaa ggtatgatcg cagcaatcgt gattggttta
      481 gttgttggta ttatttattc aatggccttt aatcgtaatt gggttatcaa actacctgat
      541 agtgtgcctg aaggggtatc caatgcattt aaatcgctta ttcctggttt tcttattatc
      601 actcttgctt tcttaacgta tatcttcttt gaagttgtat ttgaaagaac ctttattgaa
      661 accatttatc atattattca aacaccacta caaagcatgt ctgattcatt ctttggagcg
      721 gttggtattg ctttgcttat ttctctgctt tggtggtgtg gtgttcatgg tccagttatt
      781 gttatgggca tcatgggacc aatcgtgact gcgaacgcac ttcataatca atctatcgtt
      841 aatgcaggcg aagcattgat tgctggcgaa aatggcaaag tggtaactaa ccagtttgtt
      901 gaccaattca ttactgttgg cggttcaggt ctaacgtttg gtttagtgtg ctgtatggtg
      961 ttatttgctc gttctattca gttcaaacaa cttggtcgtc tttcttttat cccaggtatt
     1021 ttcaatatca atgaacctgt gatttttgca actccaatta tctttaaccc aatcatgttt
     1081 attccatttg taacagcacc agtgctatca gcaattatgg tttatacgtc aattaatatg
     1141 ggatttgttg gtccatttac cgcagttcaa gtgccttgga caacgcctat ggtgcttagc
     1201 ggattcatcg ttggtggttg gagtgcagca ttactacaaa tagccgtgtt ctgtatgaca
     1261 gtgtgcgttt atttcccatt ctttaaatat caagacaagt tagcagctca agatgaagca
     1321 aaggcagcag cgccaacatc acaagcaaca gcttaattaa aacagattag atgagtatcg
     1381 aggttattat gaaaaagatt ttattactat gtgcagcagg tatgtctacg tcaatggttg
     1441 taaaaaaaat gcgtgaatca gcagaacaaa aaggactaga tattcatatc gaagcccacg
     1501 gtgttgaaac gattcaagac tatttatctg aatatgattt attcctatta gggccacaaa
     1561 ttcgttttaa aaaagatgaa cttcagaaac tggcagatga agtaaataag aaagtcgaag
     1621 tcatcgacat gatggattac ggcatgatga aaggcgagaa gattctaaat gatgcattgg
     1681 ctcttttaga ctaacaatat tcagttggct acagtaatag acaggaattt gaaatgaaat
     1741 ttgcacatga ttttttattt ggcgcagcaa ccgcttctta tcaagtggaa ggcgcgtggg
     1801 atcaagatgg taaaggtcct acaaactggg atgagtttac taaaatacca ggaaaaacgt
     1861 ttgaaggaac taacggtgat gtcgcggttg atcattacaa tcgttataaa gaagacatcg
     1921 ctttaatggc ggaaatgggg ttagagtcat accgtttttc aatttcttgg gctcgtattt
     1981 tcccaaatgg aacgggtgaa attaaccaaa aaggcatcga tttttataat aatctgatcg
     2041 atgaatgttt gaaatatggc attgttcctt ttgttaccct atatcactgg gatctgccat
     2101 tagcactaga aaaagaaggt gcatggttaa ataaagcaac gggcgatgcg tatgtcgagt
     2161 tcgctaaatt atgtttcaac gaattcggtg accgtgttaa gcattttata acgtttaatg
     2221 aaacggttgt gttctgtgct ctaggatata tggcaggcgc acacccacca ggcattcaaa
     2281 atgacccgaa aaaatacttc caagcaacac ataacgtatt ttacgctcat gctaaagcag
     2341 tgattgaata taaaaaatta aatcaatttg gtgagattgg tttgagtcat gtatttagcc
     2401 ctgcatttgg ggttgatgat tctgaagaga gtcactttgc tgcaatgcat gcgaatcaat
     2461 ttagtatgaa ctggttctat gatcctattt tgcttggtaa atacccagag tatgtagtta
     2521 agcaattaca agaagaaggt aaccttcctg attggacgga tgaagagcta caaactattt
     2581 ttgaagccgc acctttgaat gactttatgg gattgaatta ttaccagcct cagcgtgtag
     2641 agaaaattca aggggatgtt gaagctcgta cgattacacg agaaaactca acgggctcac
     2701 ctggtaaccc tagttacgat aatgtgtacc gtactgtgaa aatggcagat aaaaagtaca
     2761 cgaaatggga ttgggaaatt tcacctgaag ggtttgttgg cggattagaa atgctgaaag
     2821 agcactatgg tcaaattaaa ctctacatca cggaaaatgg tttaggtgat gaagatccaa
     2881 tcattgaagg tgaagtgtgc gatattccac gtattaattt tattaaagag cacttaggtg
     2941 cggtaaaaga agcggttcgt cgtggtgttc atattaaagg gtattacgct tggtctgcca
     3001 ttgacttatt aagttggtta aatggttata aaaagcaata tggttttatc tatgtagatc
     3061 atcaaaatgg attggctcgt aagaaaaaag catcattcca ctggtttaaa gatgtcatag
     3121 ccactcgtgg tgaagatatt taactgaaat aaagagagaa gttcgcatta tggcaacgta
     3181 catttcgttt gatattggtg gtacagacat aaagtttggc gtgttaaatg aacaaggaaa
     3241 agttcttgag caagggaaag tgaaaactga aacttgcgga gaaaaaatca ttgccactct
     3301 tgtggatata aaagagcagt ggtcaaaaaa gtatacgttc gatggtgcag ctttctctct
     3361 tcctggattt gtagatgtaa acacagggta tttaaaaacg ggtggagcaa ttgatgattt
     3421 ctacggtttt caatttaaag atgaattaac caagaagtta tcgttacctg ttgaattaga
     3481 gaatgatgtt aactgtgtag cgcttgctga aaaatggctc ggtaaagcac aacatgttga
     3541 gaattttatc tgtattacga taggcacagg tattggtggt gctatctata ttaataatca
     3601 aatggttcga ggtcatggct ttatggctgg agagtttggt tatatgttta caagaaatgt
     3661 atttgatatt gaagataaag caacagcaag tatgagtttt actgcatcag tcagagaagg
     3721 gttaagacgt cgttattcaa cattaaaaaa tattaatagt attgataata tatcaggaaa
     3781 agatattttt gaactcgcat caacaggtga tgaagtagca ataaaagtaa ttgatgactt
     3841 ttataataat attgctatcg gtttatataa ccttacgttt attttaaatc cagaaaaaat
     3901 aattattggt ggagcgataa gtagtcgaga agatttgatt tctaatattg aaaagaaatt
     3961 taatcagatt attaaaagcc aaagttcaat taatgaattt aatgttaaag agttagtttc
     4021 cattgagaaa agtacattta ataatgacag tggattaatt ggagcggtat atcacttttt
     4081 aacaatgaaa aacaaattta aataggaata aagaatatgc tagtcggtga agagttagaa
     4141 actacagtaa tggaacttat tattaatgca ggtgaatcta aatcatgtgc aatggaagcg
     4201 ttacgagcag caaaatctgg cgaatgggat aaagttgatg atcttttaaa gcaatcagct
     4261 gaagcttcga aaagagcgca tgatgtgcaa acacagctta ttggcatgga tgagggagaa
     4321 ggaaaagtgc ctgtaaattt aattatggtg cacgcccaag atcatattat gacctctatg
     4381 cttgcaaaag agatgattca agagctaatt gagattcatc gcgcgttgca gaataaataa
     4441 taaagtgtat ttagcgtaat aacttagcta ttattacgct aatttcatct acatattttt
     4501 gagggctcaa tggcaacaat caatgacgta tgtaagcttg caggtgtttc taaagcgacc
     4561 gtttctcgag taatgaatgg aaaaggtcca gtaaaagaag aaacaaaaaa actgattttt
     4621 gatgcaatgg aaacattaga ctataaaccg agccttgtcg ctcaagcatt ggcaacaaat
     4681 agttctaata gtattggcct tattgtgtcg ttctttgatg gttattattt tggtatttta
     4741 ctcaaagaag cgacaagaat tgcagaagaa tcaggaaagc aattaatcgt cactgacggt
     4801 cataatcaag ttgaaactga gatcgaagcc attaattcac tagtggcaag aaagtgtgat
     4861 gctattttaa tttatagtcg cacgatgacg gctgatgatt attgcgaaat tcagaaaaaa
     4921 ctgccgatcc cacttgttgt tattaatcga accttacctg atggcttagg gcacgcagtt
     4981 gcttttgacc aatataatgc aagtcaaatg gctattgagc atcttgttgg attagggcat
     5041 aaaaacattg cgattatcac ccttaatatg acatcaagta ctggtcaaat tcgcttgaaa
     5101 ggagcgaaag aaacgcttga aaaacatggt attgcttatg atgataactt aaccataata
     5161 aagaatggta agttagaaga tgggtatcaa gcatgtaaag agttgctgaa gcgttcacaa
     5221 gatatttctg ctattttttg ttttaatgat catttagcac tcggtgcaat taaagcctta
     5281 aaagagatga atattcgtgt tcctgaagat atttccatcg ttgggataga taatgatgag
     5341 atttctgcat ttttatctcc agcgttaaca acgattaata ttcctattca aaaagtaact
     5401 cagttggcaa tggataaagc attgagattg atttctgata aagaagtaaa agcaacaact
     5461 gaaatattaa aaggtaatat aattgttcgt gaatcaacaa agaatattaa ttaa
//
