Furfurilactobacillus rossiae strain L1 plasmid LROSL1_p1, complete sequence.
type: Entry
definition: Furfurilactobacillus rossiae strain L1 plasmid LROSL1_p1, complete sequence.
sequence version: NZ_CP040580.1
sequence date: 2022-10-24
sequence: sequence
division: CON
label: NZ_CP040580.1
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\nCP040580.1.\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: 9470
topology: circular
so has quality: SO_0000988
location: 1..9470
location: region:1-9470:1
RO_0002162: 231049

NZ_CP040580
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:9470:1
position: 9470
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-9470:1:source
so part of: sequence
organism: Furfurilactobacillus rossiae
mol type: genomic DNA
strain: L1
isolation source: swine's gut
plasmid: LROSL1_p1
country: Italy
collection date: 2016-04-11

231049
type: Taxonomy
SIO_000068: taxonomy

LROSL1_RS13205
type: Gene
subclass of: SO_0000704
RO_0002162: 231049
locus tag: LROSL1_RS13205
so part of: sequence
location: complement(join(9458..9470,1..92))
location: region:1-9470:-1
so has part: feature:1-92:-1:exon
so has part: feature:9458-9470:-1:exon
subclass of: SO_0000010

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

position:9470:-1
position: 9470
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-92:-1:exon

position:92:-1
position: 92
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:9458-9470:-1:exon

position:9458:-1
position: 9458
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

LROSL1_RS13205
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 231049
locus tag: LROSL1_RS13205
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
GO function: GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO process: GO:0006313 - transposition, DNA-mediated [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: transposase
translation: MSGIKRHLAVDINGLPMAVHVTTANVSERDGFRQ
SIO_010081: LROSL1_RS13205
subclass of: SO_0000673
so part of: LROSL1_RS13205
location: complement(join(9458..9470,1..92))
location: region:1-9470:-1
so has part: feature:1-92:-1:exon
so has part: feature:9458-9470:-1:exon

WP_263863235.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-92:-1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:9458-9470:-1:exon

LROSL1_RS13210
type: Gene
subclass of: SO_0000704
RO_0002162: 231049
locus tag: LROSL1_RS13210
old locus tag: LROSL1_p10001
so part of: sequence
location: complement(155..493)
location: region:155-493:-1
so has part: feature:155-493:-1:exon
subclass of: SO_0000010

position:155:-1
position: 155
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:493:-1
position: 493
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:155-493:-1:exon

LROSL1_RS13210
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 231049
locus tag: LROSL1_RS13210
old locus tag: LROSL1_p10001
inference: COORDINATES: protein motif:HMM:NF024736.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: IS5 family transposase
translation: MKSFAHHYSSDISREQFELIRTDLEGIRKRTKPRKVDLYDIFCALLYTLKNGCVWRDLPSDFPKWETVYYYWLLWTKTPSPAGITPLDKVLKKLSANIGWLRSVQFIHRSSF
SIO_010081: LROSL1_RS13210
subclass of: SO_0000673
so part of: LROSL1_RS13210
location: complement(155..493)
location: region:155-493:-1
so has part: feature:155-493:-1:exon

WP_011031953.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:155-493:-1:exon

LROSL1_RS00010
type: Gene
subclass of: SO_0000704
RO_0002162: 231049
locus tag: LROSL1_RS00010
pseudo: true
so part of: sequence
location: 751..>840
location: region:751-840:1
so has part: feature:751-840:1:exon
subclass of: SO_0000010

position:751:1
position: 751
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:840:1
position: 840
reference: sequence
type: ForwardStrandPosition
type: FuzzyPosition

urn:…
SIO_000300: 1
SIO_000628: feature:751-840:1:exon

LROSL1_RS00010
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 231049
locus tag: LROSL1_RS00010
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_RS00010
subclass of: SO_0000673
so part of: LROSL1_RS00010
location: 751..>840
location: region:751-840:1
so has part: feature:751-840:1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:751-840:1:exon

LROSL1_RS00015
type: Gene
subclass of: SO_0000704
RO_0002162: 231049
locus tag: LROSL1_RS00015
old locus tag: LROSL1_p10002
so part of: sequence
location: complement(882..1349)
location: region:882-1349:-1
so has part: feature:882-1349:-1:exon
subclass of: SO_0000010

position:882:-1
position: 882
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1349:-1
position: 1349
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:882-1349:-1:exon

LROSL1_RS00015
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 231049
locus tag: LROSL1_RS00015
old locus tag: LROSL1_p10002
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_RS00015
subclass of: SO_0000673
so part of: LROSL1_RS00015
location: complement(882..1349)
location: region:882-1349:-1
so has part: feature:882-1349:-1:exon

WP_003587210.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:882-1349:-1:exon

LROSL1_RS00020
type: Gene
subclass of: SO_0000704
RO_0002162: 231049
locus tag: LROSL1_RS00020
old locus tag: LROSL1_p10004
so part of: sequence
location: complement(2515..4080)
location: region:2515-4080:-1
so has part: feature:2515-4080:-1:exon
subclass of: SO_0000010

position:2515:-1
position: 2515
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4080:-1
position: 4080
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2515-4080:-1:exon

LROSL1_RS00020
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 231049
locus tag: LROSL1_RS00020
old locus tag: LROSL1_p10004
inference: COORDINATES: protein motif:HMM:NF020498.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: DUF1906 domain-containing protein
translation: MANLHKNVADGIVSFRKFMKLPPYTSTADLTVIKGLLTSNGNTNRSSDGVDMATQITSAATAKSLKAAGYNIIGRYLTGSVGTGADKRDKNLTNTEVKLLLDANLKIFPIYEDGGYEESYFNSKQGFADASIAVNTARQLGLPSGTVIYFAVDVDIQDGNMSSTVVPYFEGITGIIGSTEYKAGIYGTRNACLHVNHLVKYSFVADMSSGWSGNLGFKMPENWSFDQFNEFTGASTGIDMDQVAVSGKDNGVSKVTKVNINPNAAFFTQLQQVEDQAYSYISGESSSTPAEQLVTQFYRQFSYSSPSWAPLAGGLNTSWLAFANSALHVSKESDFETLYDSTTGIKIGLPHMMASLNALLFWGEPQSASGIQDLGGWCGDLLTSIEDAHLNQKKYGSFYESITAYVGNKGQFGREDLVDDLDALNVYSTIHSQNNQTISKIIKTYYTGNESSVRFNSYLSNRFDDDLDSLQNDTYTLLKGGTGSWGAAYKTALLAFKKFKLQNILLILTVKQKTPLKLFAS
SIO_010081: LROSL1_RS00020
subclass of: SO_0000673
so part of: LROSL1_RS00020
location: complement(2515..4080)
location: region:2515-4080:-1
so has part: feature:2515-4080:-1:exon

WP_225440503.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2515-4080:-1:exon

LROSL1_RS13165
type: Gene
subclass of: SO_0000704
RO_0002162: 231049
locus tag: LROSL1_RS13165
old locus tag: LROSL1_p10005
so part of: sequence
location: complement(4034..4795)
location: region:4034-4795:-1
so has part: feature:4034-4795:-1:exon
subclass of: SO_0000010

position:4034:-1
position: 4034
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4795:-1
position: 4795
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4034-4795:-1:exon

LROSL1_RS13165
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 231049
locus tag: LROSL1_RS13165
old locus tag: LROSL1_p10005
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MDEMVKETQVWLNKTYGKVSGFGKVPEDGNTGWNTVYGLTRALQHELGITDLVDNFGPSTAAKWDTQFANKVKTGFKHNVVKIIQGGFWCKGINPEDFTGEFTTNTAAAVVELKKDAGIKDTSANVNSDIMKALLTMSAFVLVPGGDAKIRSMQQQLNHDYQAYTGILPCDGIYQRDTNTALIYALQSVEGMDTGTANGYYGPGTINKTPTVNSGATGAIVKIIQYGLYVNGFYSGAFNGQFTQKCCRRYSFL
SIO_010081: LROSL1_RS13165
subclass of: SO_0000673
so part of: LROSL1_RS13165
location: complement(4034..4795)
location: region:4034-4795:-1
so has part: feature:4034-4795:-1:exon

WP_225440504.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4034-4795:-1:exon

LROSL1_RS00025
type: Gene
subclass of: SO_0000704
RO_0002162: 231049
locus tag: LROSL1_RS00025
old locus tag: LROSL1_p10006
so part of: sequence
location: complement(5156..5503)
location: region:5156-5503:-1
so has part: feature:5156-5503:-1:exon
subclass of: SO_0000010

position:5156:-1
position: 5156
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5503:-1
position: 5503
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5156-5503:-1:exon

LROSL1_RS00025
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 231049
locus tag: LROSL1_RS00025
old locus tag: LROSL1_p10006
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_RS00025
subclass of: SO_0000673
so part of: LROSL1_RS00025
location: complement(5156..5503)
location: region:5156-5503:-1
so has part: feature:5156-5503:-1:exon

WP_178913281.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5156-5503:-1:exon

LROSL1_RS00030
type: Gene
subclass of: SO_0000704
RO_0002162: 231049
locus tag: LROSL1_RS00030
old locus tag: LROSL1_p10007
so part of: sequence
location: complement(5503..5766)
location: region:5503-5766:-1
so has part: feature:5503-5766:-1:exon
subclass of: SO_0000010

position:5766:-1
position: 5766
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5503-5766:-1:exon

LROSL1_RS00030
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 231049
locus tag: LROSL1_RS00030
old locus tag: LROSL1_p10007
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_RS00030
subclass of: SO_0000673
so part of: LROSL1_RS00030
location: complement(5503..5766)
location: region:5503-5766:-1
so has part: feature:5503-5766:-1:exon

WP_001748062.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5503-5766:-1:exon

LROSL1_RS00035
type: Gene
subclass of: SO_0000704
RO_0002162: 231049
locus tag: LROSL1_RS00035
old locus tag: LROSL1_p10008
so part of: sequence
location: 5845..6432
location: region:5845-6432:1
so has part: feature:5845-6432:1:exon
subclass of: SO_0000010

position:5845:1
position: 5845
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6432:1
position: 6432
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5845-6432:1:exon

LROSL1_RS00035
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 231049
locus tag: LROSL1_RS00035
old locus tag: LROSL1_p10008
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_RS00035
subclass of: SO_0000673
so part of: LROSL1_RS00035
location: 5845..6432
location: region:5845-6432:1
so has part: feature:5845-6432:1:exon

WP_001748063.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5845-6432:1:exon

LROSL1_RS00040
type: Gene
subclass of: SO_0000704
RO_0002162: 231049
locus tag: LROSL1_RS00040
old locus tag: LROSL1_p10010
so part of: sequence
location: 7775..8710
location: region:7775-8710:1
so has part: feature:7775-8710:1:exon
subclass of: SO_0000010

position:7775:1
position: 7775
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:8710:1
position: 8710
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7775-8710:1:exon

LROSL1_RS00040
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 231049
locus tag: LROSL1_RS00040
old locus tag: LROSL1_p10010
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_RS00040
subclass of: SO_0000673
so part of: LROSL1_RS00040
location: 7775..8710
location: region:7775-8710:1
so has part: feature:7775-8710:1:exon

WP_001748065.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:7775-8710:1:exon

LROSL1_RS00045
type: Gene
subclass of: SO_0000704
RO_0002162: 231049
locus tag: LROSL1_RS00045
old locus tag: LROSL1_p10011
so part of: sequence
location: 8703..9221
location: region:8703-9221:1
so has part: feature:8703-9221:1:exon
subclass of: SO_0000010

position:8703:1
position: 8703
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:9221:1
position: 9221
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:8703-9221:1:exon

LROSL1_RS00045
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 231049
locus tag: LROSL1_RS00045
old locus tag: LROSL1_p10011
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_RS00045
subclass of: SO_0000673
so part of: LROSL1_RS00045
location: 8703..9221
location: region:8703-9221:1
so has part: feature:8703-9221:1:exon

WP_001748066.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:8703-9221:1:exon