Acidovorax temperans strain LMJ plasmid pEP1, complete sequence.
Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; Comamonadaceae; Acidovorax.
De novo assembly of the genome of a novel bacterial strain: Acidovorax temperans strain LMJ
Submitted (02-FEB-2023) Department of Natural Sciences, University of West Georgia, 1601 Maple street, Carrollton, GA 30118, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP117194.1.\nBacteria and source DNA available from Dr. Mautusi Mitra Professor,\nUniversity of West Georgia; Department of Natural Sciences, Biology\nBuilding,1601 Maple Street, Carrollton, GA 30118, USA.\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 Date :: 2022\nAssembly Method :: HGAP v. 4.0; FLYE v. 2.9.1\nAssembly Name :: UWG_Atem_1\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 2535.72x\nSequencing Technology :: PacBio Sequel\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/12/2023 18:13:56\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.4\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 4,461\nCDSs (total) :: 4,396\nGenes (coding) :: 4,236\nCDSs (with protein) :: 4,236\nGenes (RNA) :: 65\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 50\nncRNAs :: 3\nPseudo Genes (total) :: 160\nCDSs (without protein) :: 160\nPseudo Genes (ambiguous residues) :: 0 of 160\nPseudo Genes (frameshifted) :: 45 of 160\nPseudo Genes (incomplete) :: 116 of 160\nPseudo Genes (internal stop) :: 22 of 160\nPseudo Genes (multiple problems) :: 22 of 160\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
Acidovorax temperans strain LMJ was isolated from a contaminated Tris Acetate Phosphate (TAP) medium culture plate of the green micro-alga Chlamydomonas reinhardtii strain, LMJ.SG0182 (a Chlamydomonas Library project (CLiP) strain)
COORDINATES: similar to AA sequence:RefSeq:WP_012435588.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_015060658.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_086558120.1
GO:0006313 - transposition, DNA-mediated [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: similar to AA sequence:RefSeq:WP_008904918.1
COORDINATES: similar to AA sequence:RefSeq:WP_011465930.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_000100290.1
COORDINATES: similar to AA sequence:RefSeq:WP_021138877.1
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:NF012798.2
COORDINATES: similar to AA sequence:RefSeq:WP_008902918.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_007853328.1
type II toxin-antitoxin system HipA family toxin YjjJ
COORDINATES: protein motif:HMM:NF017832.2
COORDINATES: protein motif:HMM:NF024949.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011485815.1
COORDINATES: similar to AA sequence:RefSeq:WP_012479493.1
COORDINATES: protein motif:HMM:NF023168.2
COORDINATES: protein motif:HMM:TIGR01865.1
GO:0005575 - cellular_component [Evidence IEA]
GO:0004520 - endodeoxyribonuclease activity [Evidence IEA]
GO:0043571 - maintenance of CRISPR repeat elements [Evidence IEA]
Cas9, originally named Csn1, is the large, multifunctional signature protein of type II CRISPR/Cas systems. It is well known even to general audiences because its RNA-guided endonuclease activity has made it a popular tool for custom editing of eukaryotic genomes.; Cas9, originally named Csn1, is the large, multifunctional signature protein of type II CRISPR/Cas systems. It is well known even to general audiences because its RNA-guided endonuclease activity has made it a popular tool for custom editing of eukaryotic genomes; Derived by automated computational analysis using gene prediction method: Protein Homology.
type II CRISPR RNA-guided endonuclease Cas9
COORDINATES: similar to AA sequence:RefSeq:WP_006029611.1
COORDINATES: protein motif:HMM:NF016343.2
COORDINATES: similar to AA sequence:RefSeq:WP_014028938.1
COORDINATES: protein motif:HMM:TIGR03639.1
GO:0004519 - endonuclease activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
GO:0051607 - defense response to virus [Evidence IEA]; GO:0043571 - maintenance of CRISPR repeat elements [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012655174.1
GO:0004521 - endoribonuclease activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012655322.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_001278583.1
COORDINATES: similar to AA sequence:RefSeq:WP_013262640.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516288.1
COORDINATES: similar to AA sequence:RefSeq:WP_019643115.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: protein motif:HMM:NF040493.1
COORDINATES: similar to AA sequence:RefSeq:WP_019574207.1
COORDINATES: similar to AA sequence:RefSeq:WP_007513924.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_086558039.1
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_057597905.1
COORDINATES: protein motif:HMM:NF037161.2
COORDINATES: similar to AA sequence:RefSeq:WP_059669267.1
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_011486166.1
COORDINATES: similar to AA sequence:RefSeq:WP_043387407.1
IS5-like element ISAav2 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_008652562.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015012600.1
COORDINATES: similar to AA sequence:RefSeq:WP_003053047.1
electron transfer flavoprotein subunit beta/FixA family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010107262.1
COORDINATES: similar to AA sequence:RefSeq:WP_008348205.1
substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012838032.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0016614 - oxidoreductase activity, acting on CH-OH group of donors [Evidence IEA]
GMC family oxidoreductase N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012252028.1
GO:0003824 - catalytic activity [Evidence IEA]; GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]
FAD-linked oxidase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_034400331.1
COORDINATES: similar to AA sequence:RefSeq:WP_012778778.1
COORDINATES: similar to AA sequence:RefSeq:WP_012838031.1
COORDINATES: similar to AA sequence:RefSeq:WP_012838030.1
COORDINATES: similar to AA sequence:RefSeq:WP_012838029.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_013395480.1
COORDINATES: similar to AA sequence:RefSeq:WP_008348195.1
branched-chain amino acid ABC transporter ATP-binding protein/permease
COORDINATES: similar to AA sequence:RefSeq:WP_008348193.1
branched-chain amino acid ABC transporter permease
COORDINATES: similar to AA sequence:RefSeq:WP_012416179.1
ABC transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF017269.2
GO:0019867 - outer membrane [Evidence IEA]
glycine zipper 2TM domain-containing protein
COORDINATES: protein motif:HMM:NF025052.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016301 - kinase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003052529.1
COORDINATES: similar to AA sequence:RefSeq:WP_024945956.1
COORDINATES: similar to AA sequence:RefSeq:WP_013899954.1
four-helix bundle copper-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_011805111.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
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: similar to AA sequence:RefSeq:WP_013104584.1
GO:0015074 - DNA integration [Evidence IEA]
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008063281.1
Cd(II)/Pb(II)-responsive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_018288532.1
COORDINATES: similar to AA sequence:RefSeq:WP_008902885.1
COORDINATES: protein motif:HMM:NF014273.2
ParB N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF020535.2
COORDINATES: similar to AA sequence:RefSeq:WP_044398522.1
COORDINATES: protein motif:HMM:NF013753.2
COORDINATES: protein motif:HMM:NF040570.1
COORDINATES: similar to AA sequence:RefSeq:WP_018465161.1
COORDINATES: similar to AA sequence:RefSeq:WP_011831576.1
COORDINATES: protein motif:HMM:NF013235.2
COORDINATES: protein motif:HMM:NF022432.2
IS630-like element ISStma10 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_076611904.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013516282.1
COORDINATES: similar to AA sequence:RefSeq:WP_010106168.1
COORDINATES: similar to AA sequence:RefSeq:WP_011483563.1
type II toxin-antitoxin system HipA family toxin
COORDINATES: protein motif:HMM:NF024491.2
phospholipase D-like domain-containing protein
COORDINATES: protein motif:HMM:NF015639.2
COORDINATES: protein motif:HMM:NF013014.2
COORDINATES: similar to AA sequence:RefSeq:WP_008902895.1
COORDINATES: similar to AA sequence:RefSeq:WP_001902481.1
COORDINATES: similar to AA sequence:RefSeq:WP_008902897.1
flagellar basal body-associated FliL family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003465043.1
COORDINATES: similar to AA sequence:RefSeq:WP_011514928.1
GO:0020037 - heme binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011342942.1
type II toxin-antitoxin system mRNA interferase toxin, RelE/StbE family
COORDINATES: similar to AA sequence:RefSeq:WP_011342941.1
COORDINATES: similar to AA sequence:RefSeq:WP_003159187.1
COORDINATES: similar to AA sequence:RefSeq:WP_017172645.1
COORDINATES: similar to AA sequence:RefSeq:WP_019334760.1
COORDINATES: similar to AA sequence:RefSeq:WP_009602860.1
COORDINATES: similar to AA sequence:RefSeq:WP_001370723.1
Tn3-like element IS1071 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_011516065.1
COORDINATES: similar to AA sequence:RefSeq:WP_019574237.1
nickel-dependent hydrogenase large subunit
COORDINATES: similar to AA sequence:RefSeq:WP_018314859.1
COORDINATES: similar to AA sequence:RefSeq:WP_020162824.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0005506 - iron ion binding [Evidence IEA]
GO:0022904 - respiratory electron transport chain [Evidence IEA]
Ni/Fe-hydrogenase, b-type cytochrome subunit
COORDINATES: similar to AA sequence:RefSeq:WP_018412539.1
COORDINATES: similar to AA sequence:RefSeq:WP_018227496.1
HyaD/HybD family hydrogenase maturation endopeptidase
COORDINATES: similar to AA sequence:RefSeq:WP_011516059.1
HypC/HybG/HupF family hydrogenase formation chaperone
COORDINATES: similar to AA sequence:RefSeq:WP_019916022.1
COORDINATES: similar to AA sequence:RefSeq:WP_018314855.1
hydrogenase expression/formation protein
COORDINATES: similar to AA sequence:RefSeq:WP_011516056.1
COORDINATES: similar to AA sequence:RefSeq:WP_018412533.1
[NiFe]-hydrogenase assembly chaperone HybE
COORDINATES: similar to AA sequence:RefSeq:WP_008973570.1
COORDINATES: similar to AA sequence:RefSeq:WP_011801354.1
hydrogenase maturation nickel metallochaperone HypA
COORDINATES: similar to AA sequence:RefSeq:WP_011516052.1
GO:0016530 - metallochaperone activity [Evidence IEA]; GO:0000166 - nucleotide binding [Evidence IEA]
GO:0036211 - protein modification process [Evidence IEA]
hydrogenase nickel incorporation protein HypB
COORDINATES: similar to AA sequence:RefSeq:WP_018314850.1
COORDINATES: similar to AA sequence:RefSeq:WP_011289688.1
COORDINATES: similar to AA sequence:RefSeq:WP_018314848.1
GO:0016530 - metallochaperone activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018227507.1
hydrogenase expression/formation protein HypE
COORDINATES: similar to AA sequence:RefSeq:WP_018314845.1
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008063435.1
sigma-54 dependent transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008063432.1
COORDINATES: similar to AA sequence:RefSeq:WP_019915998.1
GO:0016151 - nickel cation binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011830380.1
COORDINATES: similar to AA sequence:RefSeq:WP_013953000.1
GO:0004332 - fructose-bisphosphate aldolase activity [Evidence IEA]
GO:0006096 - glycolytic process [Evidence IEA]
catalyzes the reversible aldol condensation of dihydroxyacetonephosphate and glyceraldehyde 3-phosphate in the Calvin cycle, glycolysis, and/or gluconeogenesis; catalyzes the reversible aldol condensation of dihydroxyacetonephosphate and glyceraldehyde 3-phosphate in the Calvin cycle, glycolysis, and/or gluconeogenesis; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_015914613.1
COORDINATES: similar to AA sequence:RefSeq:WP_011801376.1
GO:0006094 - gluconeogenesis [Evidence IEA]; GO:0019682 - glyceraldehyde-3-phosphate metabolic process [Evidence IEA]; GO:0006096 - glycolytic process [Evidence IEA]
type I glyceraldehyde-3-phosphate dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_019429720.1
GO:0016787 - hydrolase activity [Evidence IEA]
GO:0008152 - metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011801374.1
GO:0004802 - transketolase activity [Evidence IEA]
GO:0006098 - pentose-phosphate shunt [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011463693.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0008974 - phosphoribulokinase activity [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009521584.1
GO:0042132 - fructose 1,6-bisphosphate 1-phosphatase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019429724.1
GO:0004750 - D-ribulose-phosphate 3-epimerase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020066366.1
COORDINATES: similar to AA sequence:RefSeq:WP_011829079.1
COORDINATES: similar to AA sequence:RefSeq:WP_011829078.1
ribulose bisphosphate carboxylase small subunit
COORDINATES: similar to AA sequence:RefSeq:WP_009858946.1
form I ribulose bisphosphate carboxylase large subunit
COORDINATES: similar to AA sequence:RefSeq:WP_019429734.1
COORDINATES: similar to AA sequence:RefSeq:WP_011674462.1
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_009238030.1
COORDINATES: similar to AA sequence:RefSeq:WP_009238029.1
COORDINATES: similar to AA sequence:RefSeq:WP_009238028.1
COORDINATES: similar to AA sequence:RefSeq:WP_009238027.1
COORDINATES: similar to AA sequence:RefSeq:WP_009238026.1
COORDINATES: similar to AA sequence:RefSeq:WP_009238025.1
GO:0051139 - metal cation:proton antiporter activity [Evidence IEA]
CusA/CzcA family heavy metal efflux RND transporter
COORDINATES: similar to AA sequence:RefSeq:WP_009238024.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_009238023.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009238021.1
COORDINATES: similar to AA sequence:RefSeq:WP_012840053.1
GO:0000155 - phosphorelay sensor kinase activity [Evidence IEA]; GO:0004673 - protein histidine kinase activity [Evidence IEA]; GO:0016772 - transferase activity, transferring phosphorus-containing groups [Evidence IEA]
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0016310 - phosphorylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003055031.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
heavy metal response regulator transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_009238019.1
COORDINATES: similar to AA sequence:RefSeq:WP_009238018.1
COORDINATES: similar to AA sequence:RefSeq:WP_009238017.1
COORDINATES: similar to AA sequence:RefSeq:WP_018310970.1
COORDINATES: similar to AA sequence:RefSeq:WP_003151133.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
type II toxin-antitoxin system RelE/ParE family toxin