Secundilactobacillus paracollinoides strain TMW 1.1979 plasmid pL11979-1, complete sequence.
Bacteria; Bacillota; Bacilli; Lactobacillales; Lactobacillaceae; Secundilactobacillus.
Pediococcus and Lactobacillus from brewery environment - whole genome sequencing and assembly
Submitted (18-MAR-2016) Technische Mikrobiologie, Technische Universitaet Muenchen, Gregor-Mendel-Strasse 4, Freising, Bavaria 85354, Germany
REFSEQ INFORMATION: The reference sequence is identical to\nCP014913.1.\nSource DNA or bacteria available from the culture collection of the\nTechnische Mikrobiologie Weihenstephan upon request and only if\npermitted by a potential cooperation partner. Individual decisions.\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 Method :: Celera Assembler v. 1\nAssembly Name :: Lparacoll11979-1\nLong Assembly Name :: Lactobacillus paracollinoides TMW 1.1979 1\nGenome Coverage :: 107\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 10/22/2022 03:23:05\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) :: 3,009\nCDSs (total) :: 2,917\nGenes (coding) :: 2,822\nCDSs (with protein) :: 2,822\nGenes (RNA) :: 92\nrRNAs :: 7, 6, 6 (5S, 16S, 23S)\ncomplete rRNAs :: 7, 6, 6 (5S, 16S, 23S)\ntRNAs :: 70\nncRNAs :: 3\nPseudo Genes (total) :: 95\nCDSs (without protein) :: 95\nPseudo Genes (ambiguous residues) :: 0 of 95\nPseudo Genes (frameshifted) :: 51 of 95\nPseudo Genes (incomplete) :: 28 of 95\nPseudo Genes (internal stop) :: 22 of 95\nPseudo Genes (multiple problems) :: 5 of 95\nCRISPR Arrays :: 3\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_013728233.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF024835.2
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF012920.2
COORDINATES: protein motif:HMM:NF025826.2
COORDINATES: similar to AA sequence:RefSeq:WP_015474353.1
COORDINATES: similar to AA sequence:RefSeq:WP_015474677.1
COORDINATES: similar to AA sequence:RefSeq:WP_020089731.1
RNA-guided endonuclease TnpB family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003607724.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003645724.1
COORDINATES: similar to AA sequence:RefSeq:WP_015639781.1
COORDINATES: similar to AA sequence:RefSeq:WP_011222016.1
COORDINATES: protein motif:HMM:NF013357.2
GO:0003796 - lysozyme activity [Evidence IEA]
GO:0016998 - cell wall macromolecule catabolic process [Evidence IEA]; GO:0009253 - peptidoglycan catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013355633.1
frameshifted; internal stop; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003108378.1
COORDINATES: similar to AA sequence:RefSeq:WP_013727908.1
programmed frameshift; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013728366.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012655.2
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_014940246.1
hydrophobe/amphiphile efflux-3 (HAE3) family transporter
COORDINATES: protein motif:HMM:NF017524.2
plasmid mobilization relaxosome protein MobC
COORDINATES: protein motif:HMM:NF015397.2
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015639714.1
COORDINATES: similar to AA sequence:RefSeq:WP_007124949.1
COORDINATES: similar to AA sequence:RefSeq:WP_010620856.1
COORDINATES: protein motif:HMM:NF014533.2
COORDINATES: similar to AA sequence:RefSeq:WP_002834562.1
type II toxin-antitoxin system YafQ family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_003586674.1
type II toxin-antitoxin system prevent-host-death family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_005917937.1
COORDINATES: similar to AA sequence:RefSeq:WP_003636737.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_001748276.1
COORDINATES: similar to AA sequence:RefSeq:WP_004563097.1
GO:0030612 - arsenate reductase (thioredoxin) activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013721068.1
arsenite efflux transporter metallochaperone ArsD
COORDINATES: similar to AA sequence:RefSeq:WP_003682896.1
COORDINATES: similar to AA sequence:RefSeq:WP_016368213.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0015446 - ATPase-coupled arsenite transmembrane transporter activity [Evidence IEA]
GO:0071722 - detoxification of arsenic-containing substance [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003582114.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: protein motif:HMM:NF013676.2
COORDINATES: similar to AA sequence:RefSeq:WP_002313310.1
COORDINATES: similar to AA sequence:RefSeq:WP_016526818.1
COORDINATES: similar to AA sequence:RefSeq:WP_020090467.1
COORDINATES: similar to AA sequence:RefSeq:WP_002403444.1
GO:0006304 - DNA modification [Evidence IEA]
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013579.2
COORDINATES: similar to AA sequence:RefSeq:WP_011241744.1
type II toxin-antitoxin system PemK/MazF family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_003715897.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015083018.1
COORDINATES: similar to AA sequence:RefSeq:WP_002833133.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
phage terminase small subunit P27 family
COORDINATES: similar to AA sequence:RefSeq:WP_002833134.1
GO:0004519 - endonuclease activity [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: similar to AA sequence:RefSeq:WP_003638317.1
COORDINATES: protein motif:HMM:TIGR01671.1
COORDINATES: similar to AA sequence:RefSeq:WP_004165760.1
COORDINATES: similar to AA sequence:RefSeq:WP_015076549.1
COORDINATES: similar to AA sequence:RefSeq:WP_016381988.1
PD-(D/E)XK nuclease-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008360781.1
GO:0006259 - DNA metabolic process [Evidence IEA]