LOCUS NC_015421 10798 bp DNA circular CON 11-SEP-2023
DEFINITION Lentilactobacillus buchneri NRRL B-30929 plasmid pLBUC03, complete
sequence.
ACCESSION NC_015421
VERSION NC_015421.1
DBLINK BioProject: PRJNA224116
BioSample: SAMN00713605
Assembly: GCF_000211375.1
KEYWORDS GSC:MIGS:2.1; RefSeq.
SOURCE Lentilactobacillus buchneri NRRL B-30929
ORGANISM Lentilactobacillus buchneri NRRL B-30929
Bacteria; Bacillota; Bacilli; Lactobacillales; Lactobacillaceae;
Lentilactobacillus.
REFERENCE 1 (bases 1 to 10798)
AUTHORS Liu,S., Leathers,T.D., Copeland,A., Chertkov,O., Goodwin,L. and
Mills,D.A.
TITLE Complete genome sequence of Lactobacillus buchneri NRRL B-30929, a
novel strain from a commercial ethanol plant
JOURNAL J Bacteriol 193 (15), 4019-4020 (2011)
PUBMED 21622751
REFERENCE 2 (bases 1 to 10798)
AUTHORS Lucas,S., Copeland,A., Lapidus,A., Cheng,J.-F., Goodwin,L.,
Pitluck,S., Chertkov,O., Detter,J.C., Han,C., Tapia,R., Land,M.,
Hauser,L., Kyrpides,N., Ivanova,N., Mikhailova,N., Pagani,I.,
Leathers,T.D., Mills,D., Liu,S. and Woyke,T.
CONSRTM US DOE Joint Genome Institute
TITLE Complete sequence of plasmid3 of Lactobacillus buchneri NRRL
B-30929
JOURNAL Unpublished
REFERENCE 3 (bases 1 to 10798)
AUTHORS Lucas,S., Copeland,A., Lapidus,A., Cheng,J.-F., Goodwin,L.,
Pitluck,S., Chertkov,O., Detter,J.C., Han,C., Tapia,R., Land,M.,
Hauser,L., Kyrpides,N., Ivanova,N., Mikhailova,N., Pagani,I.,
Leathers,T.D., Mills,D., Liu,S. and Woyke,T.
CONSRTM US DOE Joint Genome Institute
TITLE Direct Submission
JOURNAL Submitted (12-APR-2011) US DOE Joint Genome Institute, 2800
Mitchell Drive B310, Walnut Creek, CA 94598-1698, USA
COMMENT REFSEQ INFORMATION: The reference sequence is identical to
CP002655.1.
URL -- http://www.jgi.doe.gov
JGI Project ID: 4086509
Source DNA and organism available from Siqing Liu
(Siqing.Liu@ars.usda.gov)
Contacts: Siqing Liu (Siqing.Liu@ars.usda.gov)
Tanja Woyke (microbe@cuba.jgi-psf.org)
Annotation done by JGI-ORNL and JGI-PGF
Finishing done by JGI-LANL
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/
##MIGS-Data-START##
investigation_type :: bacteria_archaea
project_name :: Lactobacillus buchneri NRRL B-30929
collection_date :: Missing
lat_lon :: Missing
depth :: Missing
alt_elev :: Missing
country :: Missing
environment :: Host, Intestinal microflora
num_replicons :: 4
ref_biomaterial :: NRRL B-30929
biotic_relationship :: Free living
trophic_level :: Missing
rel_to_oxygen :: Facultative
isol_growth_condt :: Missing
sequencing_meth :: WGS
assembly :: Newbler v. 2.3 (pre-release)
finishing_strategy :: Finished
GOLD Stamp ID :: Gi02021
Funding Program :: DOEM 2007
Isolation Site :: Fuel ethanol production facility
Cell Shape :: Rod-shaped
Motility :: Nonmotile
Temperature Range :: Mesophile
Gram Staining :: Gram+
Diseases :: None
Phenotypes :: Probiotic
##MIGS-Data-END##
##Genome-Assembly-Data-START##
Finishing Goal :: Finished
Current Finishing Status :: Finished
Assembly Method :: Newbler v. 2.3
Genome Coverage :: 30x
Sequencing Technology :: Sanger/454/Illumina
##Genome-Assembly-Data-END##
##Genome-Annotation-Data-START##
Annotation Provider :: NCBI RefSeq
Annotation Date :: 09/11/2023 01:05:54
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) :: 2,542
CDSs (total) :: 2,461
Genes (coding) :: 2,419
CDSs (with protein) :: 2,419
Genes (RNA) :: 81
rRNAs :: 5, 5, 5 (5S, 16S, 23S)
complete rRNAs :: 5, 5, 5 (5S, 16S, 23S)
tRNAs :: 63
ncRNAs :: 3
Pseudo Genes (total) :: 42
CDSs (without protein) :: 42
Pseudo Genes (ambiguous residues) :: 0 of 42
Pseudo Genes (frameshifted) :: 20 of 42
Pseudo Genes (incomplete) :: 15 of 42
Pseudo Genes (internal stop) :: 8 of 42
Pseudo Genes (multiple problems) :: 1 of 42
CRISPR Arrays :: 1
##Genome-Annotation-Data-END##
COMPLETENESS: full length.
FEATURES Location/Qualifiers
source 1..10798
/organism="Lentilactobacillus buchneri NRRL B-30929"
/mol_type="genomic DNA"
/strain="NRRL B-30929"
/db_xref="taxon:511437"
/plasmid="pLBUC03"
gene 494..1597
/locus_tag="LBUC_RS12565"
/old_locus_tag="Lbuc_2447"
CDS 494..1597
/locus_tag="LBUC_RS12565"
/old_locus_tag="Lbuc_2447"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_007124949.1"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="replication initiator protein A"
/protein_id="WP_013721104.1"
/translation="MDQTNFKFYQADNVYGALFFQFPKVLMYSQQYRGLSDAAKLAYM
VLKDRLEYSLRNHWIDEEGHVYFIFTNQELKDLFDCSNDKLAAVKKDLERAGLLYQKA
MHFNPKTGKNEPNRLYLAELDMQSTDVYLRGEYAQKEPQTLATSENPKIGRSRETAQT
LATSENPKIGHSRKFVDDNPQTLATSENPKIGHDLYKDFKNIDTNRYNIDTQKLDFST
AHFSPEEIQKQNQDLVNHANDFLTDEDSGLPVFLEPEAVQLLSFWCRTPQQMRRFIGI
ILNAKYRVEKDHQDIGVLIPLDDEELKPLMTKALRRYFNALRSNEKHIKNVENYLYGT
MQNLFSIYWNKKANAKYQAEHSKTSHQKAALFN"
gene 1885..2094
/locus_tag="LBUC_RS12570"
/old_locus_tag="Lbuc_2448"
CDS 1885..2094
/locus_tag="LBUC_RS12570"
/old_locus_tag="Lbuc_2448"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_003554896.1"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="hypothetical protein"
/protein_id="WP_013721105.1"
/translation="MSKKIWIVIFRYLLAIGLFLAYSALFDNQDHDLIRSTLVFAICL
GLAIIPFRSCPRSMIFDILLCKKRV"
gene 2098..2885
/locus_tag="LBUC_RS12995"
/old_locus_tag="Lbuc_2449"
CDS join(2098..2356,2356..2885)
/locus_tag="LBUC_RS12995"
/old_locus_tag="Lbuc_2449"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_013727908.1"
/ribosomal_slippage
/GO_function="GO:0004803 - transposase activity [Evidence
IEA]"
/note="programmed frameshift; Derived by automated
computational analysis using gene prediction method:
Protein Homology."
/codon_start=1
/transl_table=11
/product="IS5 family transposase"
/protein_id="WP_080487858.1"
/translation="MKNYPSNITRQQFELIRPALENFRKRTKPRKYDLYEVFCAVLYV
LKTGCQWRQVPGDFPEWRSVYNYYKIWSTKAEPTADSLLEQVFKKIVIARRTYQGRSA
LTSFIIVDAQSVKNTATAENKGYDAGKKISGIKRHLAVDINGFPQAIHMTRANVSDRD
GASAMIALHAMHLRQVQNVLVDGGYSGVNFQLDVASNLNATVQVAKRNELHRFEVMPQ
RWVVERSFSWLENCRRLWKNCERQLTTSLQMVVLAFLALLLKRF"
gene complement(3283..3648)
/locus_tag="LBUC_RS12585"
/old_locus_tag="Lbuc_2450"
CDS complement(3283..3648)
/locus_tag="LBUC_RS12585"
/old_locus_tag="Lbuc_2450"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_015083018.1"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="hypothetical protein"
/protein_id="WP_013721106.1"
/translation="MDLDFKTNKYELFDDWHQNKTKQEFTQKLQQQAQIEKTHLPKLL
SREDLKIRWQMNSRQSVHQVASKPDFPQPVFAFNHGKTPLYLETEIQIFEINHPWVIT
PSARLAYSHWILRNVIDQS"
gene complement(3661..4248)
/locus_tag="LBUC_RS12590"
/old_locus_tag="Lbuc_2451"
CDS complement(3661..4248)
/locus_tag="LBUC_RS12590"
/old_locus_tag="Lbuc_2451"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_005917937.1"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="site-specific integrase"
/protein_id="WP_013721107.1"
/translation="MQQVVLPIKDSNVLKEVQDTLLNNFKAGRRNYTVFQVGKATLLR
VSDVMRLKQADIFNPDGSIKQNAFIHDRKTGKPNTLYLKPVQTELLLYRQWLLDHRLA
TEWLFPSIQHPERHITEKQFYKIMSKVGDLLGINYLGTHTMRKTGAYRVYTQSNYNIG
LVMNLLNHSSEAMTLAYLGLDQASTETMLDQIDFG"
gene 4325..4603
/locus_tag="LBUC_RS12595"
/old_locus_tag="Lbuc_2452"
CDS 4325..4603
/locus_tag="LBUC_RS12595"
/old_locus_tag="Lbuc_2452"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_003586674.1"
/GO_process="GO:0008219 - cell death [Evidence IEA]"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="type II toxin-antitoxin system
prevent-host-death family antitoxin"
/protein_id="WP_003586674.1"
/translation="MTLALTQSDFRANLKKYLDQVNDEDETVYIARSNSRAVAIVSQE
KMDWLERALKAKEGSLEYAIARDQLIKRHVLPDDEIVESDDDYWGQFK"
gene 4603..4959
/locus_tag="LBUC_RS12600"
/old_locus_tag="Lbuc_2453"
CDS 4603..4959
/locus_tag="LBUC_RS12600"
/old_locus_tag="Lbuc_2453"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_002834562.1"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="type II toxin-antitoxin system YafQ family
toxin"
/protein_id="WP_002834562.1"
/translation="MKKLRFKPRATFNADLKRLASLDKSIIDEVRAAIDLLLEQQQLP
PEFEDHELNRRMSGYNEFHLRDTPKNKTPSETNDVLVVYTIDKDELVLIGIRVGSHDR
LFPGQNRSKRYRKNDE"
gene complement(5070..5486)
/gene="arsC"
/locus_tag="LBUC_RS12605"
/old_locus_tag="Lbuc_2454"
CDS complement(5070..5486)
/gene="arsC"
/locus_tag="LBUC_RS12605"
/old_locus_tag="Lbuc_2454"
/EC_number="1.20.4.4"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_013721108.1"
/GO_function="GO:0030612 - arsenate reductase
(thioredoxin) activity [Evidence IEA]"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="arsenate reductase (thioredoxin)"
/protein_id="WP_013721108.1"
/translation="MKKIYFLCTGNSCRSQMAEGYAKELFPSDKFEIRSAGVEKHGLN
KNAVQVMAEDGVDISQQYSKLIDLNYFNSANLIVTLCGDARDKCPVIPPQATSIHWPL
PDPAKATGTEKEKLQAFKKVRNKIKDNLFELVQNYK"
gene 5587..6507
/locus_tag="LBUC_RS12610"
/old_locus_tag="Lbuc_2455"
CDS 5587..6507
/locus_tag="LBUC_RS12610"
/old_locus_tag="Lbuc_2455"
/function="4.5 Transposon and IS"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_011373852.1"
/GO_function="GO:0004803 - transposase activity [Evidence
IEA]"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="IS30-like element ISLsa1 family transposase"
/protein_id="WP_011373852.1"
/translation="MGTSTLSRFQRGALAQLVNEGNKSYQVMADALGVAKATISYELD
RVKPYDPELAQQDADRKRRNCGRRSMLTAALATLITNHLRLTWSPETIAAAYNLSTAS
IYNWLNRGWLPFKLTDLPNRNVRQHRVSENRGKFTSGTSIEQRPTTVNQRLAFGHWEV
DTVLSSRSESRSCLVTFVERKTRLLWAIKAPNRTAKALNTAFGKFMGAFGPQVKSITV
DHGKEFANYQALEQDYQIKVYFCHPYSPWERGSNEYFNRRLRWFFPKKTNFSQVTTDE
ILAALELINQRPLKIHHQQTAIERFRACSD"
gene complement(6535..7509)
/gene="arsB"
/locus_tag="LBUC_RS12615"
CDS complement(6535..7509)
/gene="arsB"
/locus_tag="LBUC_RS12615"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_010761752.1"
/GO_function="GO:0008490 - arsenite secondary active
transmembrane transporter activity [Evidence IEA]"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="ACR3 family arsenite efflux transporter"
/protein_id="WP_049775823.1"
/translation="MALGIISGLAFPSLPKIINSWSIGTTSIPIAIGLILMLYPPLTK
VNYGKMGDVFKDKKELAFSLVQNWIVGPILMFALAVIFLHNYPNYMIGLIMIGLARCI
AMVIVWNELAQGNNDYAAGLVAFNSIFQILLYSVYAYFFISVLPKFFGLQTQTINITM
SEIAKSVFIYLGIPFILGIGSRYFIISTKGKEWFEDKYVPKISRITTWALLFTIVVMF
SVKGAKVVQLPMDAIRIAVPLLLYFVLMFFITFWIAKKTKTSYSISATQSFTAASNNF
ELAVAVTVAIFGLNSGEAFAAVIGPMVEVPVMILLVDVALWIKRKYYD"
gene complement(7536..8323)
/locus_tag="LBUC_RS13000"
/old_locus_tag="Lbuc_2457"
CDS complement(join(7536..8065,8065..8323))
/locus_tag="LBUC_RS13000"
/old_locus_tag="Lbuc_2457"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_013727908.1"
/ribosomal_slippage
/GO_function="GO:0004803 - transposase activity [Evidence
IEA]"
/note="programmed frameshift; Derived by automated
computational analysis using gene prediction method:
Protein Homology."
/codon_start=1
/transl_table=11
/product="IS5 family transposase"
/protein_id="WP_080487858.1"
/translation="MKNYPSNITRQQFELIRPALENFRKRTKPRKYDLYEVFCAVLYV
LKTGCQWRQVPGDFPEWRSVYNYYKIWSTKAEPTADSLLEQVFKKIVIARRTYQGRSA
LTSFIIVDAQSVKNTATAENKGYDAGKKISGIKRHLAVDINGFPQAIHMTRANVSDRD
GASAMIALHAMHLRQVQNVLVDGGYSGVNFQLDVASNLNATVQVAKRNELHRFEVMPQ
RWVVERSFSWLENCRRLWKNCERQLTTSLQMVVLAFLALLLKRF"
gene complement(8481..8798)
/locus_tag="LBUC_RS12630"
/old_locus_tag="Lbuc_2458"
CDS complement(8481..8798)
/locus_tag="LBUC_RS12630"
/old_locus_tag="Lbuc_2458"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_012391388.1"
/GO_function="GO:0003677 - DNA binding [Evidence IEA]"
/GO_function="GO:0003700 - DNA-binding transcription
factor activity [Evidence IEA]"
/GO_process="GO:0006355 - regulation of DNA-templated
transcription [Evidence IEA]"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="metalloregulator ArsR/SmtB family transcription
factor"
/protein_id="WP_012391388.1"
/translation="MHYEYKDLASLLKVVAEPNRLKILEMLSCGEMCGCDILAHFNFT
QPTLSHHMSILEKSGLVNVRKDTKWHYYSLNSNKKEGLISELTQILSKTDHCICKDSH
SNC"
gene 9305..9652
/locus_tag="LBUC_RS12635"
/old_locus_tag="Lbuc_2459"
CDS 9305..9652
/locus_tag="LBUC_RS12635"
/old_locus_tag="Lbuc_2459"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_010620858.1"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="DUF3139 domain-containing protein"
/protein_id="WP_010620858.1"
/translation="MLKKIGYVIALLLGFFLIVWLAIYWQHRTYFTGAVRTYMVAQKI
PKNSIKNQKIVFNWVNMGQWEEDVSIRHQHHTYQYIYNMSWQDKRVSLSIYDHREGVK
DTLAPYPPLEYDR"
gene complement(10061..10627)
/locus_tag="LBUC_RS12645"
/old_locus_tag="Lbuc_2461"
CDS complement(10061..10627)
/locus_tag="LBUC_RS12645"
/old_locus_tag="Lbuc_2461"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_010620856.1"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="DUF536 domain-containing protein"
/protein_id="WP_013721110.1"
/translation="MGKTIRQLSEEFKLSKQAINQRINSINGFRSKHTYKVKNHLEID
NQGVKMLADFDKQKRQERQPNRQDENDKDKNINHILLKQLDVKDQQIENLQQALDQQQ
KLQIATVSENHRLKEHVRKLSGLLDSSSATQQQKSNDKDDVLSNNVNTRHSKDKNDKQ
NENRVAEYNNRQKKVSKNKVNNSWWRFW"
CONTIG join(CP002655.1:1..10798)
//
