Pediococcus inopinatus strain DSM 20285 plasmid pLDW-12, complete sequence.
Bacteria; Bacillota; Bacilli; Lactobacillales; Lactobacillaceae; Pediococcus.
The whole genome sequencing and assembly of Pediococcus inopinatus DSM 20285T strain
Submitted (02-MAR-2017) Kyungpook National University, School of applied Biosciences, 80 Daehak-ro, bukgu, Daegu 41566, South Korea
REFSEQ INFORMATION: The reference sequence is identical to\nCP019982.1.\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/\nThis genome has a base modification file available.\n\n##Genome-Assembly-Data-START##\nAssembly Method :: SMRT analysis 2.3 v. HGAP protocol 2\nGenome Coverage :: 396.94\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/28/2023 02:40:07\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.5\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 2,331\nCDSs (total) :: 2,252\nGenes (coding) :: 2,198\nCDSs (with protein) :: 2,198\nGenes (RNA) :: 79\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 63\nncRNAs :: 4\nPseudo Genes (total) :: 54\nCDSs (without protein) :: 54\nPseudo Genes (ambiguous residues) :: 0 of 54\nPseudo Genes (frameshifted) :: 21 of 54\nPseudo Genes (incomplete) :: 23 of 54\nPseudo Genes (internal stop) :: 14 of 54\nPseudo Genes (multiple problems) :: 4 of 54\nCRISPR Arrays :: 1\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_003687972.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003636225.1
putative sulfate exporter family transporter
COORDINATES: protein motif:HMM:NF013753.2
COORDINATES: similar to AA sequence:RefSeq:WP_013727908.1
GO:0004803 - transposase activity [Evidence IEA]
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_014569099.1
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_020807835.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_050892470.1
ISL3-like element IS1165 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_003649837.1
COORDINATES: similar to AA sequence:RefSeq:WP_003649838.1
COORDINATES: similar to AA sequence:RefSeq:WP_003712525.1
COORDINATES: similar to AA sequence:RefSeq:WP_005693113.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
type II toxin-antitoxin system RelB/DinJ family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_010620892.1
COORDINATES: similar to AA sequence:RefSeq:WP_007124583.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016301 - kinase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003603789.1
COORDINATES: similar to AA sequence:RefSeq:WP_012552807.1
COORDINATES: similar to AA sequence:RefSeq:WP_016511122.1
COORDINATES: similar to AA sequence:RefSeq:WP_014621624.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_076612170.1
internal stop; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_002819709.1
GO:0004601 - peroxidase activity [Evidence IEA]
GO:0006979 - response to oxidative stress [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013855178.1
COORDINATES: similar to AA sequence:RefSeq:WP_016386861.1
COORDINATES: similar to AA sequence:RefSeq:WP_053338758.1
IS30-like element ISLpl1 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_086558186.1
IS3-like element IS1163 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_020751524.1
COORDINATES: similar to AA sequence:RefSeq:WP_012212401.1
GO:0008519 - ammonium transmembrane transporter activity [Evidence IEA]
GO:0072488 - ammonium transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003637574.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010015738.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012305134.1
GO:0016798 - hydrolase activity, acting on glycosyl bonds [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020457141.1
GO:0008982 - protein-N(PI)-phosphohistidine-sugar phosphotransferase activity [Evidence IEA]
GO:0009401 - phosphoenolpyruvate-dependent sugar phosphotransferase system [Evidence IEA]
COORDINATES: protein motif:HMM:NF013677.2
COORDINATES: protein motif:HMM:NF033516.0
COORDINATES: similar to AA sequence:RefSeq:WP_003612343.1
COORDINATES: similar to AA sequence:RefSeq:WP_013727994.1
COORDINATES: similar to AA sequence:RefSeq:WP_003631123.1
COORDINATES: similar to AA sequence:RefSeq:WP_013439000.1
GlsB/YeaQ/YmgE family stress response membrane protein
COORDINATES: similar to AA sequence:RefSeq:WP_016371047.1
Asp23/Gls24 family envelope stress response protein
COORDINATES: similar to AA sequence:RefSeq:WP_003681705.1
COORDINATES: similar to AA sequence:RefSeq:WP_010493334.1
alkaline shock response membrane anchor protein AmaP
COORDINATES: similar to AA sequence:RefSeq:WP_010622504.1
COORDINATES: similar to AA sequence:RefSeq:WP_012304946.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002287843.1
COORDINATES: similar to AA sequence:RefSeq:WP_015474649.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002328814.1
COORDINATES: similar to AA sequence:RefSeq:WP_011672826.1
GO:0046872 - metal ion binding [Evidence IEA]
zinc ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_002817867.1
COORDINATES: similar to AA sequence:RefSeq:WP_002383181.1
COORDINATES: similar to AA sequence:RefSeq:WP_011373976.1
GO:0003735 - structural constituent of ribosome [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003602719.1
GO:0022625 - cytosolic large ribosomal subunit [Evidence IEA]; GO:0000315 - organellar large ribosomal subunit [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017262005.1
COORDINATES: similar to AA sequence:RefSeq:WP_005470367.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
ATP-dependent Clp protease ATP-binding subunit
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003554887.1
COORDINATES: similar to AA sequence:RefSeq:WP_012775157.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013728001.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012695418.1
COORDINATES: similar to AA sequence:RefSeq:WP_003600575.1
COORDINATES: similar to AA sequence:RefSeq:WP_016387560.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0019829 - ATPase-coupled monoatomic cation transmembrane transporter activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0015662 - P-type ion transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003582479.1
heavy-metal-associated domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014939378.1
GO:0008199 - ferric iron binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008215344.1
GO:0017118 - lipoyltransferase activity [Evidence IEA]
GO:0036211 - protein modification process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013728634.1
mandelate racemase/muconate lactonizing enzyme family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014940500.1
COORDINATES: similar to AA sequence:RefSeq:WP_014567995.1
COORDINATES: similar to AA sequence:RefSeq:WP_002825823.1
COORDINATES: protein motif:HMM:NF024729.2
GO:0015074 - DNA integration [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010010567.1
COORDINATES: similar to AA sequence:RefSeq:WP_014939206.1
GO:0008253 - 5'-nucleotidase activity [Evidence IEA]
YjjG family noncanonical pyrimidine nucleotidase
COORDINATES: similar to AA sequence:RefSeq:WP_008213113.1
COORDINATES: similar to AA sequence:RefSeq:WP_008213116.1
GO:0003984 - acetolactate synthase activity [Evidence IEA]; GO:0000287 - magnesium ion binding [Evidence IEA]; GO:0030976 - thiamine pyrophosphate binding [Evidence IEA]
GO:0034077 - butanediol metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003634048.1
GO:0047605 - acetolactate decarboxylase activity [Evidence IEA]
GO:0045151 - acetoin biosynthetic process [Evidence IEA]; GO:0006113 - fermentation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003625626.1