LOCUS       NC_013192               3976 bp    DNA     linear   CON 13-FEB-2020
DEFINITION  Leptotrichia buccalis C-1013-b, complete sequence.
ACCESSION   NC_013192
VERSION     NC_013192.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN00002593
            Assembly: GCF_000023905.1
KEYWORDS    RefSeq.
SOURCE      Leptotrichia buccalis C-1013-b
  ORGANISM  Leptotrichia buccalis C-1013-b
            Bacteria; Fusobacteria; Fusobacteriales; Leptotrichiaceae;
            Leptotrichia.
REFERENCE   1  (bases 1 to 3976)
  AUTHORS   Ivanova,N., Gronow,S., Lapidus,A., Copeland,A., Glavina Del Rio,T.,
            Nolan,M., Lucas,S., Chen,F., Tice,H., Cheng,J.F., Saunders,E.,
            Bruce,D., Goodwin,L., Brettin,T., Detter,J.C., Han,C., Pitluck,S.,
            Mikhailova,N., Pati,A., Mavrommatis,K., Chen,A., Palaniappan,K.,
            Land,M., Hauser,L., Chang,Y.J., Jeffries,C.D., Chain,P., Rohde,C.,
            Goker,M., Bristow,J., Eisen,J.A., Markowitz,V., Hugenholtz,P.,
            Kyrpides,N.C. and Klenk,H.P.
  TITLE     Complete genome sequence of Leptotrichia buccalis type strain
            (C-1013-b)
  JOURNAL   Stand Genomic Sci 1 (2), 126-132 (2009)
   PUBMED   21304648
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3976)
  AUTHORS   Lucas,S., Copeland,A., Lapidus,A., Glavina del Rio,T., Dalin,E.,
            Tice,H., Bruce,D., Goodwin,L., Pitluck,S., Kyrpides,N.,
            Mavromatis,K., Ivanova,N., Mikhailova,N., Brettin,T., Detter,J.C.,
            Han,C., Larimer,F., Land,M., Hauser,L., Markowitz,V., Cheng,J.-F.,
            Hugenholtz,P., Woyke,T., Wu,D., Gronow,S., Klenk,H.-P. and
            Eisen,J.A.
  CONSRTM   US DOE Joint Genome Institute (JGI-PGF)
  TITLE     The complete genome of Leptotrichia buccalis DSM 1135
  JOURNAL   Unpublished
REFERENCE   3  (bases 1 to 3976)
  AUTHORS   Lucas,S., Copeland,A., Lapidus,A., Glavina del Rio,T., Dalin,E.,
            Tice,H., Bruce,D., Goodwin,L., Pitluck,S., Kyrpides,N.,
            Mavromatis,K., Ivanova,N., Mikhailova,N., Brettin,T., Detter,J.C.,
            Han,C., Larimer,F., Land,M., Hauser,L., Markowitz,V., Cheng,J.-F.,
            Hugenholtz,P., Woyke,T., Wu,D., Gronow,S., Klenk,H.-P. and
            Eisen,J.A.
  CONSRTM   US DOE Joint Genome Institute (JGI-PGF)
  TITLE     Direct Submission
  JOURNAL   Submitted (10-AUG-2009) US DOE Joint Genome Institute, 2800 Mitchell
            Drive, Walnut Creek, CA 94598-1698, USA
COMMENT     ##Metadata-START##
            Organism Display Name :: Leptotrichia buccalis C-1013-b, DSM 1135
            Culture Collection ID :: DSM 1135, ATCC 14201, JCM 12969, NCTC
            GOLD Stamp ID                     :: Gi02240
            Funding Program                   :: DOE-GEBA 2007
            Gene Calling Method               :: Prodigal
            Isolation Site                    :: Supragingival calculus
            Host Name                         :: Homo sapiens
            Body Sample Site                  :: Oral
            Body Sample SubSite               :: Dental plaque
            Oxygen Requirement                :: Anaerobe
            Cell Shape                        :: Rod-shaped
            Motility                          :: Nonmotile
            Sporulation                       :: Nonsporulating
            Temperature Range                 :: Mesophile
            Temperature Optimum               :: 37C
            Gram Staining                     :: gram-
            Biotic Relationship               :: Free living
            Diseases                          :: Bacteremia, Cavitary pneumonia,
            Habitat                           :: Blood, Human oral microflora
            Phenotypes                        :: Pathogen
            ##Metadata-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/13/2020 21:28:44
            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)                     :: 2,322
            CDSs (total)                      :: 2,257
            Genes (coding)                    :: 2,168
            CDSs (with protein)               :: 2,168
            Genes (RNA)                       :: 65
            rRNAs                             :: 5, 5, 5 (5S, 16S, 23S)
            complete rRNAs                    :: 5, 5, 5 (5S, 16S, 23S)
            tRNAs                             :: 46
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 89
            CDSs (without protein)            :: 89
            Pseudo Genes (ambiguous residues) :: 0 of 89
            Pseudo Genes (frameshifted)       :: 56 of 89
            Pseudo Genes (incomplete)         :: 27 of 89
            Pseudo Genes (internal stop)      :: 26 of 89
            Pseudo Genes (multiple problems)  :: 19 of 89
            CRISPR Arrays                     :: 4
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence was derived from
            CP001685.
            URL -- http://www.jgi.doe.gov
            JGI Project ID: 4082970
            Source DNA and organism available from Hans-Peter Klenk at the
            German Collection of Microorganisms and Cell Cultures (DSMZ)
            (hans-peter.klenk@dsmz.de)
            Contacts: Jonathan A. Eisen (jaeisen@ucdavis.edu)
            David Bruce (microbe@cuba.jgi-psf.org)
            Whole genome sequencing and draft assembly at JGI-PGF
            Finishing done by JGI-LANL
            Annotation by JGI-ORNL and JGI-PGF
            The JGI and collaborators endorse the principles for the
            distribution and use of large scale sequencing data adopted by the
            larger genome sequencing community and urge users of this data to
            follow them. It is our intention to publish the work of this
            project in a timely fashion and we welcome collaborative
            interaction on the project and analysis.
            (http://www.genome.gov/page.cfm?pageID=10506376).
            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/
            10249
            Endocarditis, Septicemia
            Annotation Pipeline (PGAP)
            set; GeneMarkS-2+
            repeat_region
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..3976
                     /organism="Leptotrichia buccalis C-1013-b"
                     /mol_type="genomic DNA"
                     /strain="DSM 1135"
                     /type_material="type strain of Leptotrichia buccalis"
                     /db_xref="taxon:523794"
                     /note="type strain of Leptotrichia buccalis DSM 1135"
     gene            complement(1..1323)
                     /locus_tag="LEBU_RS07530"
                     /old_locus_tag="Lebu_1525"
     CDS             complement(1..1323)
                     /locus_tag="LEBU_RS07530"
                     /old_locus_tag="Lebu_1525"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_018449715.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="GH4"
                     /protein_id="WP_015769739.1"
                     /translation="MKKFSIVVAGGGSTFTPGIVLMLLENLDKFPIRQIKFYDNDAQRQ
                     EVIAKACDIIIKEKAPDINFVYTTDPETAFTDIDFVMAHIRVGKYAMREKDEKIPLRHG
                     VLGQETCGPGGISYGMRSIGGVIELVDYMEKYSPNAWMLNYSNPAAIVAEATRRLRPNS
                     KILNICDMPIGIEIRMAEMLGLKSRKDMVIRYFGLNHFGWWTDIRDKKGNDLMPALREK
                     VAKIGYNVEIEGENTEASWNDTFTKARDVFAIDPTTMPNTYLKYYFFPDYVVEHSNPNH
                     TRANEVMEGREKFVFGECRAIAEKGTAKDSKLHVDDHASYIVDLARAIAYDTKERMLLI
                     VENDGAISNFDPTAMVEVPCIVGSNGPEKIVQGKIPQFQKGLMEQQVSVEKLTVEAWME
                     GSYQKLWQAITLSRTVPSASVAKAILDDLIEANKDFWPVLK"
     gene            1550..2257
                     /locus_tag="LEBU_RS07535"
                     /old_locus_tag="Lebu_1526"
     CDS             1550..2257
                     /locus_tag="LEBU_RS07535"
                     /old_locus_tag="Lebu_1526"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_018449714.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DBD-Pfam|GntR,DBD-SUPERFAMILY|0037767"
                     /protein_id="WP_015769740.1"
                     /translation="MNKYEKVYHDIKDKIKNGKLKPGDFLKKEDDLALDYNFSKLTVRK
                     ALSMLEAEGYIQKIKGKKSIILEKKNLENISLTSIQTVQEINKLQNIHLETELISLYIV
                     QGIKKLMEEFQVPESADFYKVVRTNSLNGEVLNYSTSFFDRKIVPFLNEEIAKKSIYEY
                     LEKELNLKIAYSRRDISFRKITSEEQKYLKLEDINMVVVIETHAYLSNGTLFQYETIIH
                     HPEKFTFSAIAKR"
     gene            complement(2387..3976)
                     /locus_tag="LEBU_RS07540"
                     /old_locus_tag="Lebu_1527"
     CDS             complement(2387..3976)
                     /locus_tag="LEBU_RS07540"
                     /old_locus_tag="Lebu_1527"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_018497861.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="gnl|TC-DB|C7NB69|4.A.1.1.16"
                     /protein_id="WP_015769741.1"
                     /translation="MMKKVQRFGGAMMAPVLLFAFTGIVVGLSSVFTNTEVMGKIAEEG
                     TVWYNFWYVISEGGWTVFRQMPILFAIGLPISLATKTNARACMETFALYTTFNYFVAAI
                     LKVFYGIDAAKQVADKVTGYSAIGGVPTLDTNLFGGILIAALVVYLHNKYFDKKLPDFL
                     GVFQGSVFVYIVGFVVMIPCAFLTVLIWPKFQMGISALQGFMKASGIFGVWIYTFLERI
                     LIPTGLHHFVYTPFVFGPAAVPDGIQVYWVQHIKEFAQSTQSLKSLFPQGGFALHGNSK
                     IFGAPGIALAMYATAKSDKKKAVAALLIPIIFTAVISGITEPLEFTFLFIAPVLFAVHA
                     CLAATMAATMYAFGVVGNMGGGLLDFFFLNWIPMFKNHSGTVIAQIVIGLIFTAIYFVV
                     FRFLILKMDLKTPGREDEDEEMKLYSKADYRAKHGEGDAKGGVSSAEDEYAQKGAIILE
                     ALGGKENIEELNNCATRLRVSVKDASKLLPDAAFKAAGAHGVVRKGTAIQVIIGLSVPQ
                     VRERIEEMMKKG"
ORIGIN
        1 ctatttcaac actggccaga agtctttatt tgcttcaatt aaatcatcca atattgcttt
       61 tgcaacagat gcacttggca cagttcttga taatgtaatt gcttgccaaa gtttttggta
      121 tgaaccttcc atccatgctt ctactgtcaa tttttcaact gatacttgtt gttccattaa
      181 tcctttttgg aattgaggaa ttttaccttg aactattttt tcaggtccat ttgaacctac
      241 tatacaaggc acttctacca tcgcagttgg atcaaagttt gaaattgctc cgtcattttc
      301 tactattaat aacattcttt cttttgtatc ataagcgatt gctcttgcca agtcaactat
      361 atatgaagca tgatcatcaa cgtgaagttt gctatctttt gcagttcctt tttcagcgat
      421 tgctctacat tctccaaata caaatttttc tcttccttcc attacttcat ttgctcttgt
      481 atggttagga tttgaatgtt ctactacata atcagggaag aagtagtatt ttaagtaagt
      541 attcggcatt gttgttggat caattgcaaa tacgtccctt gcttttgtaa atgtgtcatt
      601 ccagcttgct tctgtatttt ccccttcaat ttctacatta tatccaattt ttgcgacttt
      661 ttctcttaaa gcaggcatta aatcatttcc ttttttatct ctaatgtctg tccaccatcc
      721 aaagtgattt aatccaaagt atctaattac catatctttt cttgatttaa gtcctagcat
      781 ttcagccatt cttatttcaa ttccgattgg catatcacaa atatttaata ttttagagtt
      841 tggacgtaat cttctagttg cttctgctac gattgctgca ggatttgaat aatttaacat
      901 ccacgcattt ggtgaatatt tttccatata atcaactaac tcgataactc caccaattga
      961 acgcattcca taagaaattc ctccaggccc gcaagtttct tgccctaata ctccgtgtct
     1021 taaaggtatt ttttcatctt tttcacgcat tgcatatttt ccaactctta tatgtgccat
     1081 aacaaagtca atatcagtaa acgctgtttc aggatctgtt gtataaacaa agttaatatc
     1141 aggtgctttt tcctttataa taatatcaca agcctttgct ataacttcct gtctttgggc
     1201 atcattatcg taaaatttta tctgtctaat cggaaattta tctaaatttt caagtaacat
     1261 caacacaatt cctggagtaa atgtactccc tccaccagct actacaattg aaaatttctt
     1321 cataaatgat catctccatt tctattttta ttaattttta tttcctattt tcattattta
     1381 ttatatcaca atttttttaa atgtcaatac ttttatataa atcttttaaa tttttaaaaa
     1441 gaattgtata aatctttttt tattgatatt tattattatt tattgtataa tcatagtgat
     1501 aatacttaaa atcgaactta aaaattataa gaaaggttta tataaatgaa tgaataaata
     1561 tgaaaaagta tatcacgata taaaagataa aattaaaaat ggtaaactaa agcctggaga
     1621 ttttctaaaa aaagaagacg atttggcact agattataat ttttccaagc tgactgtaag
     1681 aaaagctctc tccatgctag aagcagaagg ctatattcaa aaaataaaag gtaaaaaatc
     1741 tattatactt gagaaaaaaa atctagaaaa tatttctttg acttccattc aaactgtaca
     1801 agaaattaac aagcttcaaa atattcatct tgaaactgaa ctaatcagtt tatacatcgt
     1861 tcaagggatc aaaaaactaa tggaagaatt tcaagtacct gaaagtgctg atttttataa
     1921 agttgtccgt accaattctt taaatggaga agttttaaat tattctacga gtttttttga
     1981 cagaaaaatt gtaccttttc taaatgaaga aatagcaaaa aaatcaatat atgaatatct
     2041 ggaaaaagaa cttaacctaa aaatagctta ttcacgtaga gatattagtt ttagaaaaat
     2101 tacttctgaa gaacagaaat atcttaagct agaggatata aatatggttg ttgttattga
     2161 aactcatgcc tatctttcaa atggcactct atttcaatac gaaacaatta ttcaccatcc
     2221 tgaaaaattt acttttagtg caattgcaaa aagataagta ttttaaaaat aaaagaaaga
     2281 actttcttaa gtcttatatt ttaaaacttt aaaatttttg acttttgaaa attctttctt
     2341 aattttttta taagatttaa atttaattat ttatcaaatt ttatttttat ccttttttca
     2401 tcatttcttc gattctttct cttacttgag gtactgacaa tccaatgatt acttgaattg
     2461 ctgtaccttt tctaactaca ccgtgagctc ctgccgcttt aaatgctgca tctggtaata
     2521 atttacttgc atcttttaca cttactctaa gtctagttgc acaattgtta agttcttcaa
     2581 tgttttcttt tccacctaat gcttcaagaa tgattgcacc tttttgagca tattcatctt
     2641 ctgctgatga tacgccgcct tttgcatctc cttctccatg tttagctcta taatcagctt
     2701 ttgaataaag tttcatttct tcatcttcat cttctctacc tggagttttt aaatccatct
     2761 ttagaattaa gaatctaaat acaacgaagt aaattgctgt aaatattaat cctattacta
     2821 tttgagcaat tactgttcca gagtgatttt taaacattgg tatccagttt aagaagaaga
     2881 agtctaaaag tcctccaccc atatttccaa ctactccaaa agcatacatt gttgcagcca
     2941 ttgttgcagc taaacaagca tgaactgcaa ataatactgg agctataaat aagaatgtaa
     3001 attctaatgg ttcagttata cctgaaatta ctgctgtaaa tattataggt attaataatg
     3061 ctgctacggc tttcttctta tcagattttg cagtagcgta catagcaagc gctattcccg
     3121 gtgcaccaaa tatttttgag tttccgtgta gcgcaaatcc accttgtggg aataaagatt
     3181 tcaatgattg tgtactttga gcaaattctt ttatatgttg aacccagtaa acttgaattc
     3241 catcaggtac tgctgccgga ccaaatacaa acggtgtata aacaaagtga tgtaatccag
     3301 ttggaattaa gattctttct aagaacgtat aaatccacac tccaaatatt cctgaagctt
     3361 tcataaatcc ttgtaatgca ctaattccca tttgaaattt aggccaaatt aacactgtta
     3421 agaatgcaca aggaatcata actacaaatc ctactatata tacaaatact gaaccttgga
     3481 acactcctaa gaaatcaggt aactttttgt caaaatattt gttatgtaaa tatactacta
     3541 atgctgctat taagatacca ccaaataagt ttgtatccaa tgttggaact ccacctattg
     3601 cagaatatcc tgttacttta tctgctactt gtttagctgc atctattcca taaaaaactt
     3661 ttaatattgc tgctacaaaa taattaaatg tagtatataa tgcaaatgtt tccatacatg
     3721 cccttgcatt tgtctttgtt gccaagctga ttggcaatcc aattgcgaac aatattggca
     3781 tttgtctaaa tactgtccaa ccaccttctg atatcacata ccagaaattg taccatactg
     3841 tcccttcttc agcaattttt cccataactt ctgtattagt aaatacagaa gataatccta
     3901 cgactatacc cgtgaatgca aataacagaa ccggtgccat cattgctcca ccaaatcgtt
     3961 gaaccttttt catcat
//
