Furfurilactobacillus rossiae strain L1 plasmid LROSL1_p3, complete sequence.
type: Entry
definition: Furfurilactobacillus rossiae strain L1 plasmid LROSL1_p3, complete sequence.
sequence version: NZ_CP040582.1
sequence date: 2022-10-24
sequence: sequence
division: CON
label: NZ_CP040582.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN11607496
keyword: RefSeq
source: Furfurilactobacillus rossiae
organism: Furfurilactobacillus rossiae
taxonomy: Bacteria; Bacillota; Bacilli; Lactobacillales; Lactobacillaceae; Furfurilactobacillus.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP040582.1.\nThe annotation was added by the NCBI Prokaryotic Genome Annotation\nPipeline (PGAP). Information about PGAP can be found here:\nhttps://www.ncbi.nlm.nih.gov/genome/annotation_prok/\n\n##Genome-Assembly-Data-START##\nAssembly Date :: 11-APR-2016\nAssembly Method :: HGAP protocol RS Assembly v. 2.0\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 100.97x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 10/24/2022 02:06:00\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA;\n repeat_region\nGenes (total) :: 2,638\nCDSs (total) :: 2,562\nGenes (coding) :: 2,545\nCDSs (with protein) :: 2,545\nGenes (RNA) :: 76\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 61\nncRNAs :: 3\nPseudo Genes (total) :: 17\nCDSs (without protein) :: 17\nPseudo Genes (ambiguous residues) :: 0 of 17\nPseudo Genes (frameshifted) :: 4 of 17\nPseudo Genes (incomplete) :: 11 of 17\nPseudo Genes (internal stop) :: 2 of 17\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 9572
topology: circular
so has quality: SO_0000988
location: 1..9572
location: region:1-9572:1
RO_0002162: 231049

NZ_CP040582
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN11607496
type: BioSample
SIO_000068: biosample

1
title: Lifestyle of Lactobacillus rossiae strains based on genomic, proteomic and phenome characterization
author: Bottacini, F.
author: Calabrese, F.M.
author: Siragusa, S.
author: van Sinderen, D.
author: Gobbetti, M.
author: De Angelis, M.
journal: Unpublished

2
title: Direct Submission
author: Bottacini, F.
author: Calabrese, F.M.
author: Siragusa, S.
author: van Sinderen, D.
author: Gobbetti, M.
author: De Angelis, M.
journal: Submitted (23-MAY-2019) Soil, Plant and Food Sciences, University of Bari, Via Amendola 165/a, Bari, BA 70126, Italy

position:1:1
position: 1
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:9572:1
position: 9572
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-9572:1:source
so part of: sequence
organism: Furfurilactobacillus rossiae
mol type: genomic DNA
strain: L1
isolation source: swine's gut
plasmid: LROSL1_p3
country: Italy
collection date: 2016-04-11

231049
type: Taxonomy
SIO_000068: taxonomy

LROSL1_RS00055
type: Gene
subclass of: SO_0000704
RO_0002162: 231049
locus tag: LROSL1_RS00055
old locus tag: LROSL1_p30001
so part of: sequence
location: 1..588
location: region:1-588:1
so has part: feature:1-588:1:exon
subclass of: SO_0000010

position:588:1
position: 588
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-588:1:exon

LROSL1_RS00055
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 231049
locus tag: LROSL1_RS00055
old locus tag: LROSL1_p30001
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
translation: MQQVVLPIKDSNVLKEVQDTLLNNFKAGRRNYTIFQVGKATLLRVSDVMCLKQTNIFNPNGSIKQNAFIHDKKTGKPNTLYLKPVQTDLLLYRQWLLDNQLQSEWLFPSIQHPERHITEKQFYKIMSKVGDLLSINYLGTHTMRKTGAYRVYTQSNYNIGLVMYLLNHSSEAMTLAYLGLDQASTETMLDQIDFG
SIO_010081: LROSL1_RS00055
subclass of: SO_0000673
so part of: LROSL1_RS00055
location: 1..588
location: region:1-588:1
so has part: feature:1-588:1:exon

WP_001748063.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-588:1:exon

LROSL1_RS00060
type: Gene
subclass of: SO_0000704
RO_0002162: 231049
locus tag: LROSL1_RS00060
old locus tag: LROSL1_p30002
so part of: sequence
location: 1007..1219
location: region:1007-1219:1
so has part: feature:1007-1219:1:exon
subclass of: SO_0000010

position:1007:1
position: 1007
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1219:1
position: 1219
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1007-1219:1:exon

LROSL1_RS00060
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 231049
locus tag: LROSL1_RS00060
old locus tag: LROSL1_p30002
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010620841.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MLGVTQMDEKKVLKPIDEMLADPWQVDIQELFEAFVHEPDEIKQNLYNSLYTYILQKRQEDIINRPGFVI
SIO_010081: LROSL1_RS00060
subclass of: SO_0000673
so part of: LROSL1_RS00060
location: 1007..1219
location: region:1007-1219:1
so has part: feature:1007-1219:1:exon

WP_001748064.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1007-1219:1:exon

LROSL1_RS00065
type: Gene
subclass of: SO_0000704
RO_0002162: 231049
locus tag: LROSL1_RS00065
old locus tag: LROSL1_p30003
so part of: sequence
location: 1939..2874
location: region:1939-2874:1
so has part: feature:1939-2874:1:exon
subclass of: SO_0000010

position:1939:1
position: 1939
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2874:1
position: 2874
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1939-2874:1:exon

LROSL1_RS00065
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 231049
locus tag: LROSL1_RS00065
old locus tag: LROSL1_p30003
inference: COORDINATES: similar to AA sequence:RefSeq:WP_016526818.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiation protein
translation: MGNEIIKYDPELNTIPLRKFTPVEMNLFFSIISRMRDKSDQTIRFTFDQLKELSAYKPTANNRFEDDIQRTYEKMMGLHFGRRSKSGLTREFFVLFTEFKIDGDAEEPYVDVKVYERALPLLNKLESWVRYALAEFRDLKSSYAKTMFRLLKQFRTTGYAYFSKEDFFELLDMPKSYWNSPSNVDKFVIKPIKEELTPLFRGLTVRKKYGKGRGKPVIGYSFTWKPEKKDANDFSQGQLQDERQKLFNIQHNGELTEQEKWRAIDKVKGLTLGSTEKQALADKQAEHDKKIRDQARQEALAELRKGFGNHA
SIO_010081: LROSL1_RS00065
subclass of: SO_0000673
so part of: LROSL1_RS00065
location: 1939..2874
location: region:1939-2874:1
so has part: feature:1939-2874:1:exon

WP_001748065.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1939-2874:1:exon

LROSL1_RS00070
type: Gene
subclass of: SO_0000704
RO_0002162: 231049
locus tag: LROSL1_RS00070
old locus tag: LROSL1_p30004
so part of: sequence
location: 2867..3385
location: region:2867-3385:1
so has part: feature:2867-3385:1:exon
subclass of: SO_0000010

position:2867:1
position: 2867
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3385:1
position: 3385
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2867-3385:1:exon

LROSL1_RS00070
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 231049
locus tag: LROSL1_RS00070
old locus tag: LROSL1_p30004
inference: COORDINATES: similar to AA sequence:RefSeq:WP_007745771.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: HTH domain-containing protein
translation: MPKTIRELADELGVSKQAIWQKIKRDASIDLRQFTSTKGNTVYVDVDGQKAIKAMFSNDSSTRYRQQKDDVDDNKKDAVDGQDEVKFLRNLVSEFQSEKKELHKLLDQQQRLALQDKQLLEEYKAEIKDLKALTMAPHDNSEKEVTSDKQPEPENSTPESQPKPKKWWRFGK
SIO_010081: LROSL1_RS00070
subclass of: SO_0000673
so part of: LROSL1_RS00070
location: 2867..3385
location: region:2867-3385:1
so has part: feature:2867-3385:1:exon

WP_001748066.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2867-3385:1:exon

LROSL1_RS00075
type: Gene
subclass of: SO_0000704
RO_0002162: 231049
locus tag: LROSL1_RS00075
so part of: sequence
location: complement(3425..4224)
location: region:3425-4224:-1
so has part: feature:3425-4224:-1:exon
subclass of: SO_0000010

position:3425:-1
position: 3425
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4224:-1
position: 4224
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3425-4224:-1:exon

LROSL1_RS00075
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 231049
locus tag: LROSL1_RS00075
inference: COORDINATES: similar to AA sequence:RefSeq:WP_013727908.1
ribosomal slippage: true
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
translation: MKSFAHHYSSDISREQFELIRTDLEGIRKRTKPRKVDLYDIFCALLYTLKNGCVWRDLPSDFPKWETVYYYWLLWTKTPSPAGITPLDKVFKKIVSQHRLAQKRSVYTSFIILDAQSVKNTDPAESSGYDGGKKVSGIKRHLAVDINGLPMAVHVTTANVSERDGANALLALNKSQFDLVQRVMADGGYTGNNFAQSVQAMINAEVIIAKQSDLRHGQVTPQRWVIERSFSWLGKYRRLWRNCERKLNTSKMMISLAFLRILLKRF
SIO_010081: LROSL1_RS00075
subclass of: SO_0000673
so part of: LROSL1_RS00075
location: complement(join(3425..3954,3954..4224))
location: region:3425-4224:-1
so has part: feature:3954-4224:-1:exon
so has part: feature:3425-3954:-1:exon

WP_088899809.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3954-4224:-1:exon

position:3954:-1
position: 3954
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:3425-3954:-1:exon

LROSL1_RS00080
type: Gene
subclass of: SO_0000704
RO_0002162: 231049
locus tag: LROSL1_RS00080
pseudo: true
so part of: sequence
location: 4482..>4571
location: region:4482-4571:1
so has part: feature:4482-4571:1:exon
subclass of: SO_0000010

position:4482:1
position: 4482
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4571:1
position: 4571
reference: sequence
type: ForwardStrandPosition
type: FuzzyPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4482-4571:1:exon

LROSL1_RS00080
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 231049
locus tag: LROSL1_RS00080
inference: COORDINATES: similar to AA sequence:RefSeq:WP_053338758.1
note: incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
pseudo: true
codon start: 1
transl table: 11
product: IS30 family transposase
SIO_010081: LROSL1_RS00080
subclass of: SO_0000673
so part of: LROSL1_RS00080
location: 4482..>4571
location: region:4482-4571:1
so has part: feature:4482-4571:1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:4482-4571:1:exon

LROSL1_RS00085
type: Gene
subclass of: SO_0000704
RO_0002162: 231049
locus tag: LROSL1_RS00085
old locus tag: LROSL1_p30007
so part of: sequence
location: complement(4613..5080)
location: region:4613-5080:-1
so has part: feature:4613-5080:-1:exon
subclass of: SO_0000010

position:4613:-1
position: 4613
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5080:-1
position: 5080
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4613-5080:-1:exon

LROSL1_RS00085
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 231049
locus tag: LROSL1_RS00085
old locus tag: LROSL1_p30007
inference: COORDINATES: similar to AA sequence:RefSeq:WP_003639769.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: DNA starvation/stationary phase protection protein
translation: MKYTKTKAVLNQLVADLSQMSMIIHQTHWYMRGPNFLKLHPLMDEFMEEIDSQLDVISERLIALDGSPYSTLKEMAENTKIQDWPGEWDKTTPERLAHLVDGYRYLEDLYQHGIEVSDVEKDFSTQDIFIGLKTAIEKKIWMIQAELGSAPEIDE
SIO_010081: LROSL1_RS00085
subclass of: SO_0000673
so part of: LROSL1_RS00085
location: complement(4613..5080)
location: region:4613-5080:-1
so has part: feature:4613-5080:-1:exon

WP_003587210.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4613-5080:-1:exon

LROSL1_RS00090
type: Gene
subclass of: SO_0000704
RO_0002162: 231049
locus tag: LROSL1_RS00090
old locus tag: LROSL1_p30009
so part of: sequence
location: complement(6223..8520)
location: region:6223-8520:-1
so has part: feature:6223-8520:-1:exon
subclass of: SO_0000010

position:6223:-1
position: 6223
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:8520:-1
position: 8520
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6223-8520:-1:exon

LROSL1_RS00090
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 231049
locus tag: LROSL1_RS00090
old locus tag: LROSL1_p30009
inference: COORDINATES: similar to AA sequence:RefSeq:WP_014271901.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: DUF1906 domain-containing protein
translation: MDEMVKETQVWLNKTYGKVSGFGKVPEDGNTGWNTVYGLTRALQHELGITDLVDNFGPSTAAKWDTQFANKVKTGFKHNVVKIIQGGFWCKGINPEDFTGEFTTNTAAAVVELKKDAGIKDTSANVNSDIMKALLTMSAFVLVPGGDAKIRSMQQQLNHDYQAYTGILPCDGIYQRDTNTALIYALQSVEGMDTGTANGYYGPGTINKTPTVNSGATGAIVKIIQYGLYVNGFYSGAFNGQFTQNVADGIVSFRKFMKLPPYTSTADLTVIKGLLTSNGNTNRSSDGVDMATQITSAATAKSLKAAGYNIIGRYLTGSVGTGADKRDKNLTNTEVKLLLDANLKIFPIYEDGGYEESYFNSKQGFADASIAVNTARQLGLPSGTVIYFAVDVDIQDGNMSSTVVPYFEGITGIIGSTEYKAGIYGTRNACLHVNHLVKYSFVADMSSGWSGNLGFKMPENWSFDQFNEFTGASTGIDMDQVAVSGKDNGVSKVTKVNINPNAAFFTQLQQVEDQAYSYISGESSSTPAEQLVTQFYRQFSYSSPSWAPLAGGLNTSWLAFANSALHVSKESDFETLYDSTTGIKIGLPHMMASLNALLFWGEPQSASGIQDLGGWCGDLLTSIEDAHLNQKKYGSFYESITAYVGNKGQFGREDLVDDLDALNVYSTIHSQNNQTISKIIKTYYTGNESSVRFNSYLSNRFDDDLDSLQNDTYTLLKGGTGSWGAAYKTALLAFKKFKLQKYPSYTDSEAKDAAKAFRKLIEQNA
SIO_010081: LROSL1_RS00090
subclass of: SO_0000673
so part of: LROSL1_RS00090
location: complement(6223..8520)
location: region:6223-8520:-1
so has part: feature:6223-8520:-1:exon

WP_014271901.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6223-8520:-1:exon

LROSL1_RS00095
type: Gene
subclass of: SO_0000704
RO_0002162: 231049
locus tag: LROSL1_RS00095
old locus tag: LROSL1_p30010
so part of: sequence
location: complement(8881..9228)
location: region:8881-9228:-1
so has part: feature:8881-9228:-1:exon
subclass of: SO_0000010

position:8881:-1
position: 8881
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:9228:-1
position: 9228
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:8881-9228:-1:exon

LROSL1_RS00095
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 231049
locus tag: LROSL1_RS00095
old locus tag: LROSL1_p30010
EC number: 3.1.-.-
inference: COORDINATES: similar to AA sequence:RefSeq:WP_003646106.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: type II toxin-antitoxin system PemK/MazF family toxin
translation: MKLKQGAILWINLDPAKGTETKKKRPCLVVSNDHYNRYFNTVLVVPISTSDKYRTQEKYAKSPLFIRIDNGKIHGTALLQHVRAVDPTKRSDGEVVATLSRQEISSISTKVQQFF
SIO_010081: LROSL1_RS00095
subclass of: SO_0000673
so part of: LROSL1_RS00095
location: complement(8881..9228)
location: region:8881-9228:-1
so has part: feature:8881-9228:-1:exon

WP_178913281.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:8881-9228:-1:exon

LROSL1_RS00100
type: Gene
subclass of: SO_0000704
RO_0002162: 231049
locus tag: LROSL1_RS00100
old locus tag: LROSL1_p30011
so part of: sequence
location: complement(9228..9491)
location: region:9228-9491:-1
so has part: feature:9228-9491:-1:exon
subclass of: SO_0000010

position:9491:-1
position: 9491
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:9228-9491:-1:exon

LROSL1_RS00100
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 231049
locus tag: LROSL1_RS00100
old locus tag: LROSL1_p30011
inference: COORDINATES: similar to AA sequence:RefSeq:WP_017260787.1
GO function: GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0097351 - toxin sequestering activity [Evidence IEA]
GO process: GO:0001558 - regulation of cell growth [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 PrlF family antitoxin
translation: MSAGNVTKVSSKITSKNQITIPKTVRELLKVRSTDTIEWQIEPNGKVMIVRSKPDLWQLVDEQEKKFGNLSTTEVDWGKDVESEDFD
SIO_010081: LROSL1_RS00100
subclass of: SO_0000673
so part of: LROSL1_RS00100
location: complement(9228..9491)
location: region:9228-9491:-1
so has part: feature:9228-9491:-1:exon

WP_001748062.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:9228-9491:-1:exon